Serotype of adenovirus and uses thereof

ABSTRACT

Adenovirus serotypes differ in their natural tropism. The adenovirus serotypes 2, 4, 5 and 7 all have a natural affiliation towards lung epithelia and other respiratory tissues. In contrast, serotypes 40 and 41 have a natural affiliation towards the gastrointestinal tract. The serotypes described, differ in at least capsid proteins (penton-base, hexon), proteins responsible for cell binding (fiber protein), and proteins involved in adenovirus replication. This difference in tropism and capsid protein among serotypes has led to the many research efforts aimed at redirecting the adenovirus tropism by modification of the capsid proteins.

CROSS-REFERENCE TO RELATED APPLICATIONS

This application is a divisional application of co-pending patentapplication U.S. Ser. No. 11/586,316, filed Oct. 25, 2006, now U.S.patent Ser. No. ______, which is a continuation of U.S. patentapplication Ser. No. 10/951,102, filed Sep. 27, 2004, now U.S. Pat. No.7,270,811, which application is a continuation of U.S. patentapplication Ser. No. 09/573,740, filed May 18, 2000, now U.S. Pat. No.6,913,922, issued Jul. 5, 2005, which patent claims priority under theprovisions of 35 U.S.C. § 119(e) to U.S. Provisional Patent ApplicationSer. No. 60/134,764, filed May 18, 1999, the entirety of each of whichare incorporated herein by this reference.

STATEMENT ACCORDING TO 37 C.F.R. § 1.52(e)(5) Sequence Listing Submittedon Compact Disc

Pursuant to 37 C.F.R. § 1.52(e)(1)(iii), a compact disc containing anelectronic version of the Sequence Listing has been submittedconcomitant with this application, the contents of which are herebyincorporated by reference. A second compact disc is submitted and is anidentical copy of the first compact disc. The discs are labeled “copy 1”and “copy 2,” respectively, and each disc contains one file entitled“Sequence Listing.txt” which is 69 KB and created on Sep. 22, 2004.

TECHNICAL FIELD

The invention relates generally to the field of gene therapy,particularly gene therapy involving elements derived from viruses, morein particular, elements of adenoviruses.

BACKGROUND

Adenoviruses have been proposed as suitable vehicles to deliver genes toa host. There are a number of features of adenoviruses that make themparticularly useful for the development of gene-transfer vectors forhuman gene therapy.

The adenovirus genome is well characterized. It consists of a lineardouble-stranded DNA molecule of approximately 36000 base pairs (“bp”).The adenovirus DNA contains identical Inverted Terminal Repeats (“ITRs”)of approximately 90-140 base pairs with the exact length depending onthe serotype. The viral origins of replication are within the ITRsexactly at the genome ends.

The biology of the adenoviruses is characterized in detail. Theadenovirus is not associated with severe human pathology inimmuno-competent individuals. The virus is extremely efficient inintroducing its DNA into a host cell; the virus can infect a widevariety of cells and has a broad host-range. The virus can be producedat high virus titers in large quantities.

The virus can be rendered replication defective by deletion of theearly-region 1 (E1) of the viral genome (Brody et al., 1994). Mostadenoviral vectors currently used in gene therapy have a deletion in theE1 region, where desired genetic information can be substituted.

Based on these features, preferred methods for in vivo gene transferinto human target cells make use of adenoviral vectors as gene deliveryvehicles. However, drawbacks associated with the therapeutic use ofadenoviral vectors in humans still exist. A major drawback is theexistence of widespread pre-existing immunity among the populationagainst adenoviruses. Exposure to wild-type adenoviruses is very commonin humans, as has been documented extensively (reviewed in Wadell,1984). This exposure has resulted in immune responses against most typesof adenoviruses, not alone against adenoviruses to which individualshave actually been exposed, but also against adenoviruses which havesimilar (neutralizing) epitopes. This phenomenon of pre-existingantibodies in humans, in combination with a strong secondary humoral andcellular immune response against the virus, can seriously affect genetransfer using recombinant adenoviral vectors.

To date, six different subgroups of human adenoviruses have beenproposed which in total encompasses 51 distinct adenovirus serotypes.(See, Table 1.) A serotype is defined on the basis of its immunologicaldistinctiveness as determined by quantitative neutralization with animalantisera (horse, rabbit). If neutralization shows a certain degree ofcross-reaction between two viruses, distinctiveness of serotype isassumed if A) the hemagglutinins are unrelated, as shown by lack ofcross-reaction on hemagglutination-inhibition, or B) substantialbiophysical/biochemical differences in DNA exist (Francki et al., 1991).The nine serotypes identified last (42-51) were isolated for the firsttime from HIV-infected patients (Hierholzer et al., 1988; Schnurr etal., 1993). For reasons not well understood, most of suchimmune-compromised patients shed adenoviruses that were rarely or neverisolated from immune-competent individuals (Hierholzer et al., 1988,1992; Khoo et al., 1995, De Jong et al., 1998).

The vast majority of people have had previous exposure to adenoviruses,especially the well-investigated adenovirus serotypes 5 and type 2(“Ad5” and “Ad2”) or immunologically related serotypes. Importantly,these two serotypes are also the most extensively studied for use inhuman gene therapy.

As previously stated, the usefulness of these adenoviruses orcross-immunizing adenoviruses to prepare gene delivery vehicles may beseriously hampered, since the individual to whom the gene deliveryvehicle is provided, will raise a neutralizing response to such avehicle before long.

Thus a need exists in the field of gene therapy to provide gene deliveryvehicles, preferably based on adenoviruses, which do not encounterpre-existing immunity and/or which are capable of avoiding ordiminishing neutralizing antibody responses.

DISCLOSURE HEREOF

Provided is a gene delivery vehicle comprising at least one Ad35 elementor a functional equivalent thereof, responsible for avoiding ordiminishing neutralizing activity against adenoviral elements by thehost to which the gene is to be delivered and a gene of interest. Afunctional equivalent/homologue of an Ad35 (element) for the purposeshereof is an adenovirus (element) which, like adenovirus 35, encounterspre-existing immunity in less than about 10% of the hosts to which it isadministered for the first time, or which is capable in more than about90% of the hosts to which it is administered of avoiding or diminishingthe immune response.

Throughout the world, populations of humans can have varyingpre-existing immunity profiles. For the instant disclosure, the genedelivery vehicle of choice is preferably matched with a pre-existingimmunity profile for the particular population in that geographic area.Typical examples of such adenoviruses are adenovirus serotypes 34, 26,48 and 49.

A gene delivery vehicle may be based on Ad35 or a functional homologuethereof, but it may also be based on another backbone, such as that ofadenovirus 2 or 5, so long as it comprises at least one of the elementsfrom Ad35 or a functional equivalent thereof, which leads to adiminishment of the immune response against such an Ad2 or Ad5 basedgene delivery vehicle. The gene delivery vehicle may also compriseelements from other (adeno) viruses, so long as one replaces an elementthat could lead to immunity against such a gene delivery vehicle by anelement of Ad35 or a functional homologue thereof, which has less ofsuch a drawback and which, preferably, avoids such a drawback.

As used herein, a “gene delivery vehicle” is any vehicle capable ofdelivering a nucleic acid of interest to a host cell. It will typicallycomprise an element of Ad35 or a functional equivalent of Ad35, whichhas a beneficial effect regarding the immune response against such avehicle. Basically, all other elements making up the vehicle can be anyelements known in the art or developed in the art, as long as togetherthey are capable of delivering the nucleic acid of interest. Inprinciple, the person skilled in the art can use and/or produce anyadenoviral products or production systems that can or have been appliedin the adenoviral field. Typically, the products can be made in thepackaging cells useable with, for example, Ad5, typically the vectorsbased on Ad35 can be produced and/or used in the same manner as those ofother adenoviruses, for example, Ad2 and/or Ad5.

A good overview of the possibilities of minimal vectors, packagingsystems, intracellular amplification, vector and plasmid based systemscan be found in co-pending, co-owned International Patent ApplicationPCT/NL99/00235 or U.S. Pat. No. 5,994,128 to Bout et al., incorporatedherein by reference. Non-viral delivery systems can also be providedwith elements hereof, as can viral delivery systems. Both kinds ofsystems are well known in the art in many different set-ups and dotherefore not need any further elaboration here. A review of the manydifferent systems and their properties can be found in Robbins andGhivizzani (1998) and in Prince (1998), also incorporated herein byreference.

Gene delivery vehicles typically contain a nucleic acid of interest. Anucleic acid of interest can be a gene or a functional part of a gene(wherein a gene is any nucleic acid which can be expressed) or aprecursor of a gene or a transcribed gene on any nucleic acid level (DNAand/or RNA: double or single stranded). Genes of interest are well knownin the art and typically include those encoding therapeutic proteinssuch as TPA, EPO, cytokines, antibodies or derivatives thereof, etc.

An overview of therapeutic proteins to be applied in gene therapy islisted hereinafter. They include: immune-stimulatory factors liketumor-specific antigens, cytokines, etc.; anti-angiogenic factors,non-limiting examples of which are endostatin, angiostatin, ATF-BPTICDT-6, dominant negative VEGF-mutants, etc.; angiogenic factors,non-limiting examples of which are VEGF, fibroblast growth factors,nitric oxide synthases, C-type natriuretic peptide, etc.; inflammationinhibiting proteins like soluble CD40, FasL, IL-12, IL-10, IL-4, IL-13and excreted single chain antibodies to CD4, CD5, CD7, CD52, Il-2, IL-1,IL-6, TNF, etc., or excreted single chain antibodies to the T-cellreceptor on the auto-reactive T-cells. Also, dominant negative mutantsof PML may be used to inhibit the immune response.

Furthermore, antagonists of inflammation promoting cytokines may beused, for example, IL-1RA (receptor antagonist) and soluble receptorslike sIL-1RI, sIL-1RII, sTNFRI and sTNFRII. Growth and/or immuneresponse inhibiting genes such as ceNOS, Bcl3, cactus and IκBa, β or γand apoptosis inducing proteins like the VP3 protein of chicken anemiavirus may also be used. Furthermore, suicide genes like HSV-TK, cytosinedeaminase, nitroreductase and linamerase may be used.

A nucleic acid of interest may also be a nucleic acid that can hybridizewith a nucleic acid sequence present in the host cell thereby inhibitingexpression or transcription or translation of the nucleic acid. It mayalso block through co-suppression. In short, a “nucleic acid ofinterest” is any nucleic acid that one may wish to provide a cell within order to induce a response by that cell, such as production of aprotein, inhibition of such production, apoptosis, necrosis,proliferation, differentiation, etc.

Disclosed is the use of adenovirus 35 or a functional homologue thereoffor therapeutic use, therefore, also provided is an Ad35 or a functionalhomologue thereof or a chimeric virus derived therefrom, or a genedelivery vehicle based on the virus its homologue or its chimera for useas a pharmaceutical. The serotype preferred herein, adenovirus type 35,is in itself known in the art. It is an uncommon group B adenovirus thatwas isolated from patients with acquired immunodeficiency syndrome andother immunodeficiency disorders (Flomenberg et al., 1987; De Jong etal., 1983). Ad 35 has been shown to differ from the more fullycharacterized subgroup C (including Ad2 and Ad5) with respect topathogenic properties (Basler et al., 1996). It has been suggested thatthis difference may be correlated with differences in the E3 region ofthe Ad35 genome (Basler et al., 1996). The DNA of Ad35 has beenpartially cloned and mapped (Kang et al., 1989a and b; Valderrama-Leonet al., 1985).

B-type adenovirus serotypes such as 34 and 35 have a different E3 regionthan other serotypes. Typically, this region is involved in suppressingimmune response to adenoviral products. Thus, provided is a genedelivery vehicle wherein the elements involved in avoiding ordiminishing immune response comprise Ad35 E3 expression products or thegenes encoding them or functional equivalents of either or both.

Another part of adenoviruses involved in immune responses is the capsid,in particular the penton and/or the hexon proteins. Thus, also providedis a gene delivery vehicle wherein the elements comprise at least oneAd35-capsid protein or functional part thereof, such as fiber, pentonand/or hexon proteins or a gene encoding at least one of them. It is notnecessary that a whole protein relevant for immune response be of Ad35(or a functional homologue thereof) origin. It is very well possible toinsert a part of an adenovirus fiber, penton or hexon protein intoanother fiber, penton or hexon. Thus, chimeric proteins are obtained.

It is also possible to have a penton of a certain adenovirus, a hexonfrom another and a fiber or an E3 region from yet another adenovirus. Incertain embodiments, at least one of the proteins or genes encoding themshould comprise an element from Ad35 or a functional homologue thereof,whereby the element has an effect on the immune response of the host.Thus, provided is a gene delivery vehicle hereof, which is a chimera ofAd35 with at least one other adenovirus. In this way one can also modifythe resulting virus in other aspects than the immune response alone. Onecan enhance its efficiency of infection with elements responsibletherefor; one can enhance its replication on a packaging cell, or onecan change its tropism.

Thus, for example, provided is a gene delivery vehicle having adifferent tropism than Ad35. Of course, the tropism should be alteredpreferably such that the gene delivery vehicle is deliveredpreferentially to a subset of the host's cells, i.e., the target cells.Changes in tropism and other changes that can also be applied toadenoviral or other gene delivery vehicles are disclosed in co-pending,co-owned European Patent applications Nos. 98204482.8, 99200624.7 and98202297.2, incorporated herein by reference. The present disclosurealso provides the building blocks necessary and/or useful to get to thegene delivery vehicles and/or the chimaeras, etc. This includespackaging cells such as PER.C6 (ECACC deposit number 96022940) or cellsbased thereon, but adapted for Ad35 or a functional homologue thereof;it also includes any nucleic acids encoding functional parts of Ad35 ora functional homologue thereof, such as helper constructs and packagingconstructs, as well as vectors comprising genes of interest and, forexample, an ITR, etc. Typically, the previously incorporated U.S. Pat.No. 5,994,128 to Bout et al. (Nov. 30, 1999) discloses elementsnecessary and useful for arriving at the invented gene deliveryvehicles. Thus, provided is a nucleic acid encoding at least afunctional part of a gene delivery vehicle hereof, or a virus, homologueor chimera thereof hereof. Such elements, which encode functions thatwill end up in the resulting gene delivery vehicle must comprise or beencoded by a nucleic acid encoding at least one of the Ad35 elements ora functional equivalent thereof, responsible for avoiding or diminishingneutralizing activity against adenoviral elements by the host to whichthe gene is to be delivered. Typically, the gene of interest would bepresent on the same nucleic acid that means that such a nucleic acid hassuch a gene or that it has a site for introducing a gene of interesttherein.

Typically, such a nucleic acid also comprises at least one ITR and, ifit is a nucleic acid to be packaged, also a packaging signal. However,as mentioned before necessary and useful elements and/or building blocksfor the invention can be found in the incorporated U.S. Pat. No.5,994,128 to Bout et al. A set of further improvements in the field ofproducing adenoviral gene delivery vehicles is applicant's plasmidsystem disclosed in PCT/NL99/00235 mentioned herein before. This systemworks in one embodiment as a homologous recombination of an adapterplasmid and a longer plasmid, together comprising all elements of thenucleic acid to be incorporated in the gene delivery vehicle. Thesemethods can also be applied to the presently invented gene deliveryvehicles and their building elements. Thus, also provided is a nucleicacid hereof further comprising a region of nucleotides designed oruseable for homologous recombination, preferably as part of at least oneset of two nucleic acids comprising a nucleic acid hereof, whereby theset of nucleic acids is capable of a single homologous recombinationevent with each other, which leads to a nucleic acid encoding afunctional gene delivery vehicle.

Both empty packaging cells (in which the vector to be packaged to make agene delivery vehicle hereof still has to be introduced or produced) aswell as cells comprising a vector hereof to be packaged are provided.Thus, also encompassed is a cell comprising a nucleic acid hereof or aset of nucleic acids hereof, preferably a cell which complements thenecessary elements for adenoviral replication which are absent from thenucleic acid to be packaged, or from a set of nucleic acids hereof. Ithas now been found that E1-deleted Ad35 vectors, are not capable ofreplication on cells that provide adenovirus 5 proteins in trans.Therefore, further provided is a cell capable of providing Ad35 E1proteins in trans. Such a cell is typically a human cell derived fromthe retina or the kidney. Embryonic cells, such as amniocytes, have beenshown to be particularly suited for the generation of anE1-complementing cell line. Such cells are, therefore, preferred herein.Serotype specific complementation by E1 proteins can be due to one ormore protein(s) encoded by the E1 region. It is, therefore, essentialthat at least the serotype specific protein be provided in trans in thecomplementing cell line. The non-serotype specific E1 proteins essentialfor effective complementation of an E1-deleted adenovirus can be derivedfrom other adenovirus serotypes. In certain embodiments, at least an E1protein from the E1B region of Ad35 is provided in trans to complementE1-deleted Ad35 based vectors. In one embodiment, nucleic acid encodingthe one or more serotype specific E1-proteins is introduced into thePER.C6 cell or a cell originating from a PER.C6 cell, or a similarpackaging cell complementing with elements from Ad 35 or a functionalhomologue thereof.

Encompassed is a method for producing a gene delivery vehicle,comprising expressing a nucleic acid hereof in a cell hereof andharvesting the resulting gene delivery vehicle. The above refers to thefilling of the empty packaging cell with the relevant nucleic acids. Theformat of the filled cell is, of course, also part hereof, whichprovides a method for producing a gene delivery vehicle hereof,comprising culturing a filled packaging cell (producer cell) hereof in asuitable culture medium and harvesting the resulting gene deliveryvehicle.

The resulting gene delivery vehicles obtainable by any method hereof arealso part hereof, particularly also a gene delivery vehicle which isderived from a chimera of an adenovirus and an integrating virus.

It is well known that adenoviral gene delivery vehicles do not normallyintegrate into the host genome. For long-term expression of genes in ahost cell, it is therefore preferred to prepare chimaeras that do havethat capability. Such chimaeras have been disclosed in co-pending,co-owned International Patent Application PCT/NL98/00731 incorporatedherein by reference. A very good example of a chimera of an adenovirusand an integrating virus is where the integrating virus is anadeno-associated virus. As discussed hereinbefore, other usefulchimaeras, which can also be combined with the above, are chimaeras (beit in swapping whole proteins or parts thereof or both) that havealtered tropism. A very good example thereof is a chimera of Ad 35 andAd 16, possibly with elements from, for instance, Ad 2 or Ad 5, whereinthe tropism determining part of Ad 16 or a functional equivalent thereofis used to direct the gene delivery vehicle to synoviocytes and/orsmooth muscle cells (see co-pending, co-owned European patentapplications nos. 98204482.8 and 99200624.7) incorporated herein byreference). Dendritic cells (“DC”) and hemopoietic stem cells (“HSC”)are not easily transduced with Ad2 or Ad5 derived gene deliveryvehicles. Provided is gene delivery vehicles that possess increasedtransduction capacity of DC and HSC cells. Such gene delivery vehiclesat least comprise the tissue tropism determining part of an Ad35adenovirus. Further provided is the use of a tissue tropism determiningpart of an Ad35 capsid for transducing dendritic cells and/orhemopoietic stem cells. Other B-type adenoviruses are also suited. Atissue tropism determining part comprises at least the knob and/or theshaft of a fiber protein. It is very well possible for a person skilledin the art to determine the amino acid sequences responsible for thetissue tropism in the fiber protein. Such knowledge can be used todevise chimeric proteins comprising such amino acid sequences. Suchchimeric proteins are therefore also part hereof.

DCs are very efficient antigen presenting cells. By introducing the genedelivery vehicle into such cells, the host's immune system can betriggered toward specific antigens. Such antigens can be encoded bynucleic acid delivered to the DC or by the proteins of the gene deliveryvehicle itself. The invention therefore also provides a gene deliveryvehicle with the capacity to evade the host immune system as a vaccine.The vector being capable of evading the immune system long enough toefficiently find target cells and at the same time capable of deliveringspecific antigens to antigen presenting cells thereby allowing theinduction and/or stimulation of efficient immune responses toward thespecific antigen(s). To further modulate the immune response, the genedelivery vehicle may comprise proteins and/or nucleic acids encodingsuch proteins capable of modulating an immune response. Non-limitingexamples of such proteins are found among the interleukins, adhesionmolecules, co-stimulatory proteins, the interferons, etc. Furtherprovided is a vaccine comprising a gene delivery vehicle hereof. Theinvention further provides an adenovirus vector with the capacity toefficiently transduce DC and/or HSC, the vehicle comprising at least atissue tropism determining part of Ad35. The invention further providesthe use of such delivery vehicles for the transduction of HSC and/or DCcells. Similar tissue tropisms are found among other adenoviruses ofserotype B, particularly in Ad11 and are also part hereof. Of course, itis also possible to provide other gene delivery vehicles with the tissuetropism determining part thereby providing such delivery vehicles withan enhanced DC and/or HSC transduction capacity. Such gene deliveryvehicles are therefore also part hereof.

The gene delivery vehicles hereof can be used to deliver genes ornucleic acids of interest to host cells. Such use will typically be apharmaceutical one. Such a use is included herein. Compositions suitablefor such a use are also part hereof. The amount of gene delivery vehiclethat needs to be present per dose or per infection (“m.o.i”) will dependon the condition to be treated, the route of administration (typicallyparenteral) the subject and the efficiency of infection, etc. Dosefinding studies are well known in the art and those already performedwith other (adenoviral) gene delivery vehicles can typically be used asguides to find suitable doses of the gene delivery vehicles hereof.Typically, this is also where one can find suitable excipients, suitablemeans of administration, suitable means of preventing infection with thevehicle where it is not desired, etc. Thus, provided is a pharmaceuticalformulation comprising a gene delivery vehicle hereof and a suitableexcipient, as well as a pharmaceutical formulation comprising anadenovirus, a chimera thereof, or a functional homologue thereof hereofand a suitable excipient.

BRIEF DESCRIPTION OF THE FIGURES

FIG. 1: Bar graph showing the percentage of serum samples positive forneutralization for each human wt adenovirus tested (see, Example 1 fordescription of the neutralization assay).

FIG. 2: Graph showing absence of correlation between the VP/CCID50 ratioand the percentage of neutralization.

FIG. 3: Schematic representation of a partial restriction map of Ad35(taken from Kang et al., 1989) and the clones generated to makerecombinant Ad35-based viruses.

FIG. 4: Bar graph presenting the percentage sera samples that showneutralizing activity to a selection of adenovirus serotypes. Sera werederived from healthy volunteers from Belgium and the UK.

FIG. 5: Bar graph presenting the percentage sera samples that showneutralizing activity to adenovirus serotypes 5, 11, 26, 34, 35, 48 and49. Sera were derived from five different locations in Europe and theUnited States.

FIG. 6: Sequence of human adenovirus type 35.

FIG. 7: Map of pAdApt.

FIG. 8: Map of pIPspAdapt.

FIG. 9: Map of pIPspAdapt1.

FIG. 10: Map of pIPspAdapt3.

FIG. 11: Map of pAdApt35IP3.

FIG. 12: Map of pAdApt35IP1.

FIG. 13: Schematic representation of the steps undertaken to constructpWE.Ad35.pIX-rITR.

FIG. 14: Map of pWE.Ad35.pIX-rITR.

FIG. 15: Map of pRSV.Ad35-E1.

FIG. 16: Map of PGKneopA

FIG. 17: Map of pRSVpNeo.

FIG. 18: Map of pRSVhbvNeo.

FIG. 19: Flow cytometric analyses on GFP expression in human TF-1 cells.Non-transduced TF-1 cells were used to set a background level of 1%. GFPexpression in cells transduced with Ad5, Ad5.Fib16, Ad5.Fib17,Ad5.Fib40-L, Ad5.Fib35, and Ad5.Fib51 is shown.

FIG. 20: Transduction of primary human fibroblast-like stroma. Cellswere analyzed 48 hours after a two-hour exposure to the differentchimeric fiber viruses. Shown is percentage of cells found positive forthe transgene: GFP using a flow cytometer. Non-transduced stroma cellswere used to set a background at 1%. Results of different experiments(n=3) are shown ±standard deviation.

FIG. 21: Transduction of primary human fibroblast-like stroma, CD34⁺cells and CD34⁺Lin⁻ cells. Cells were analyzed five days after atwo-hour exposure to the different chimeric fiber viruses. Shown ispercentage of cells found positive for the transgene: GFP using a flowcytometer. Non-transduced cells were used to set a background at 1%.Also shown is the number of GFP positive events divided by the totalnumber of events analyzed (between brackets).

FIG. 22: A) Flow cytometric analysis of GFP positive cells aftertransduction of CD34⁺ cells with Ad5.Fib51. All cells gated in R2-R7 arepositive for CD34 but differ in their expression of earlydifferentiation markers CD33, CD38, and CD71 (Lin). Cells in R2 arenegative for CD333, CD38, and CD71 whereas cells in R7 are positive forthese markers. To demonstrate specificity of Ad5.Fib51 the percentage ofGFP positive cells was determined in R2-R7 that proofed to decline from91% (R2) to 15% (R7). B) Identical experiment as shown under A (X-axesis R2-R7) but for the other Ad fiber chimeric viruses showing thatAd5.Fib35, and Ad5.Fib16 behave similar as Ad5.Fib51.

FIG. 23: Alignment of the chimeric fiber proteins of Ad5fib16, Ad5fib35and Ad5fib51 with the Ad5 fiber sequence.

FIG. 24: Toxicity of Adenovirus exposure to primitive human bone marrowcells and stem cells. Cell cultures were counted just before and fivedays after adenovirus transduction. Shown is the percentage of primitivehuman bone marrow cells (CD34⁺) and HSCs (CD34⁺Lin⁻) recovered ascompared to day 0.

FIG. 25: Transduction of immature DCs at a virus dose of 100 or 1000virus particles per cell. Virus tested is Ad5 and Ad5 based vectorscarrying the fiber of serotype 12 (Ad5.Fib12), 16 (Ad5.Fib 16), 28(Ad5.Fib28), 32 (Ad5.Fib32), the long fiber of 40 (Ad5.Fib40-L, 49(Ad5.Fib49), 51 (Ad5.Fib51). Luciferase transgene expression isexpressed as relative light units per microgram of protein.

FIG. 26: Flow cytometric analyses of LacZ expression on immature andmature DCs transduced with 10000 virus particles per cell of Ad5 or thefiber chimeric vectors Ad5.Fib16, Ad5.Fib40-L, or Ad5.Fib51. Percentagesof cells scored positive are shown in upper left corner of eachhistogram.

FIG. 27: Luciferase transgene expression in human immature DCs measured48 hours after transduction with 1000 or 5000 virus particles per cell.Viruses tested were fiber chimeric viruses carrying the fiber ofsubgroup B members (serotypes 11, 16, 35, and 51).

FIG. 28: GFP expression in immature human DCs 48 hours aftertransduction with 1000 virus particles per cell of Ad5, Ad5.Fib16, andAd5.Fib35. Non-transduced cells were used to set a background level ofapproximately 1% (−).

FIG. 29: Transduction of mouse and chimpanzee DCs. Luciferase transgeneexpression measured in mouse DCs 48 hours after transduction isexpressed as relative light units per microgram of protein. ChimpanzeeDCs were measured 48 hours after transduction using a flow cytometer.GFP expression demonstrates the poor transduction of Ad (35) in contrastto Ad5.Fib35 (66%).

FIG. 30: Temperature dependent growth of PER.C6. PER.C6 cells werecultured in DMEM supplemented with 10% FBS (Gibco BRL) and 10 mM MgCl₂in a 10% CO₂ atmosphere at 32° C., 37° C. or 39° C. At day 0, a total of1×10⁶ PER.C6 cells were seeded per 25 cm² tissue culture flask (Nunc)and the cells were cultured at 32° C., 37° C. or 39° C. At days 1-8,cells were counted. The growth rate and the final cell density of thePER.C6 culture at 39° C. are comparable to that at 37° C. The growthrate and final density of the PER.C6 culture at 32° C. were slightlyreduced as compared to that at 37° C. or 39° C. PER.C6 cells were seededat a density of 1×10⁶ cells per 25 cm² tissue culture flask and culturedat 32°, 37° or 39° C. At the indicated time points, cells were countedin a Burker cell counter. PER.C6 grows well at 32°, 37° and 39° C.

FIG. 31: DBP levels in PER.C6 cells transfected with pcDNA3, pcDNA3wtE2A or pcDNA3ts125E2A. Equal amounts of whole-cell extract werefractionated by SDS-PAGE on 10% gels. Proteins were transferred ontoImmobilon-P membranes and DBP protein was visualized using the αDBPmonoclonal B6 in an ECL detection system. All of the cell lines derivedfrom the pcDNA3ts125E2A transfection express the 72-kDa E2A-encoded DBPprotein (left panel: lanes 4-14; middle panel: lanes 1-13; right panel:lanes 1-12). In contrast, the only cell line derived from the pcDNAwtE2Atransfection did not express the DBP protein (left panel, lane 2). NoDBP protein was detected in extract from a cell line derived from thepcDNA3 transfection (left panel, lane 1), which serves as a negativecontrol. Extract from PER.C6 cells transiently transfected withpcDNA3ts125 (left panel, lane 3) served as a positive control for theWestern blot procedure. These data confirm that constitutive expressionof wtE2A is toxic for cells and that using the ts125 mutant of E2A cancircumvent this toxicity.

FIG. 32: Suspension growth of PER.C6ts125E2A C5-9. The tsE2A expressingcell line PER.C6tsE2A.c5-9 was cultured in suspension in serum-freeEx-cellä. At the indicated time points, cells were counted in a Burkercell counter. The results of eight independent cultures are indicated.PER.C6tsE2A grows well in suspension in serum free Ex-cellä medium.

FIG. 33: Growth curve PER.C6 and PER.C6tsE2A. PER.C6 cells orPER.C6ts125E2A (c8-4) cells were cultured at 37° C. or 39° C.,respectively. At day 0, a total of 1×10⁶ cells were seeded per 25 cm²tissue culture flask. At the indicated time points, cells were counted.The growth of PER.C6 cells at 37° C. is comparable to the growth ofPER.C6ts125E2A c8-4 at 39° C. This shows that constitutiveover-expression of ts125E2A has no adverse effect on the growth of cellsat the non-permissive temperature of 39° C.

FIG. 34: Stability of PER.C6ts125E2A. For several passages, thePER.C6ts125E2A cell line clone 8-4 was cultured at 39° C. in mediumwithout G418. Equal amounts of whole-cell extract from different passagenumbers were fractionated by SDS-PAGE on 10% gels. Proteins weretransferred onto Immobilon-P membranes and DBP protein was visualizedusing the αDBP monoclonal B6 in an ECL detection system. The expressionof ts125E2A encoded DBP is stable for at least 16 passages, which isequivalent to approximately 40 cell doublings. No decrease in DBP levelswas observed during this culture period, indicating that the expressionof ts125E2A is stable, even in the absence of G418 selection pressure.

FIG. 35: tTA activity in hygromycin resistant PER.C6/tTA (A) andPER/E2A/tTA (B) cells. Sixteen independent hygromycin resistantPER.C6/tTA cell colonies and 23 independent hygromycin resistantPER/E2A/tTA cell colonies were grown in 10 cm² wells to sub-confluencyand transfected with 2 μg of pUHC 13-3 (a plasmid that contains thereporter gene luciferase under the control of the 7xtetO promoter).One-half of the cultures were maintained in medium containingdoxycycline to inhibit the activity of tTA. Cells were harvested at 48hours after transfection and luciferase activity was measured. Theluciferase activity is indicated in relative light units (RLU) per μgprotein.

DETAILED DESCRIPTION HEREOF

As previously stated, the most extensively studied serotypes ofadenovirus are not ideally suited for delivering additional geneticmaterial to host cells. This fact is partially due to the pre-existingimmunity among the population against these serotypes. This presence ofpre-existing antibodies in humans, in combination with a strongsecondary humoral and cellular immune response against the virus willaffect adenoviral gene therapy.

Provided is the use of at least elements of a serotype and functionalhomologues thereof of adenovirus that are very suitable as gene therapyvectors. The invention also discloses an automated high-throughputscreening of all known adenovirus serotypes against sera from manyindividuals. Surprisingly, no neutralizing ability was found in any ofthe sera that were evaluated against one particular serotype, adenovirus35 (“Ad35”). This makes the serotype hereof extremely useful as a vectorsystem for gene therapy in man. Such a vector system is capable ofefficiently transferring genetic material to a human cell without theinherent problem of pre-existing immunity.

Typically, a virus is produced using an adenoviral vector (typically aplasmid, cosmid, or baculovirus vector). Such vectors are, of course,also part hereof.

Also provided are adenovirus-derived vectors that have been renderedreplication defective by deletion or inactivation of the E1 region. Agene of interest can also be inserted at, for instance, the site of E1of the original adenovirus from which the vector is derived.

The adenoviruses may contain deletions in the E1 region and insertionsof heterologous genes either linked or not to a promoter. Furthermore,the adenoviruses may contain deletions in the E2, E3 or E4 regions andinsertions of heterologous genes linked to a promoter. In these cases,E2- and/or E4-complementing cell lines are used to generate recombinantadenoviruses.

One may choose to use the Ad35 serotype itself for the preparation ofrecombinant adenoviruses to be used in gene therapy. Alternatively, onemay choose to use elements derived from the serotype hereof in suchrecombinant adenoviruses. One may, for instance, develop a chimericadenovirus that combines desirable properties from different serotypes.Some serotypes have a somewhat limited host range, but have the benefitof being less immunogenic; while others are the other way around. Somehave a problem of being of a limited virulence, but have a broad hostrange and/or a reduced immunogenicity. Such chimeric adenoviruses areknown in the art, and they are intended to be within the scope hereof.Thus, in one embodiment, provided is a chimeric adenovirus comprising atleast a part of the adenovirus genome of the present serotype, providingit with absence of pre-existing immunity, and at least a part of theadenovirus genome from another adenovirus serotype resulting in achimeric adenovirus. In this manner, the chimeric adenovirus produced issuch that it combines the absence of pre-existing immunity of theserotype hereof, to other characteristics of another serotype. Suchcharacteristics may be temperature stability, assembly, anchoring,redirected infection, production yield, redirected or improvedinfection, stability of the DNA in the target cell, etc.

A packaging cell will generally be needed in order to produce sufficientamount of adenoviruses. For the production of recombinant adenovirusesfor gene therapy purposes, several cell lines are available. Theseinclude, but are not limited to, the known cell lines PER.C6,911,293,and E1 A549.

Disclosed is the means to produce the adenovirus. Typically, one doesnot want an adenovirus batch for clinical applications to containreplication competent adenovirus. In general, therefore, it is desiredto omit a number of genes (but at least one) from the adenoviral genomeon the adenoviral vector and to supply these genes in the genome of thecell in which the vector is brought to produce chimeric adenovirus. Sucha cell is usually called a “packaging cell.” The invention thus alsoprovides a packaging cell for producing an adenovirus (a gene deliveryvehicle) hereof, comprising in trans all elements necessary foradenovirus production not present on the adenoviral vector hereof.Typically, vectors and packaging cells have to be adapted to one anotherso that they have all the necessary elements, but do not haveoverlapping elements which lead to replication competent virus byrecombination.

Thus, also provided is a kit of parts comprising a packaging cell hereofand a recombinant vector hereof wherein essentially no sequence overlapleading to recombination resulting in the production of replicationcompetent adenovirus exists between the cell and the vector.

Thus, provided is methods for producing adenovirus, which, uponapplication, will escape pre-existing humoral immunity. Such methodsinclude providing a vector with elements derived from an adenovirusserotype against which virtually no natural immunity exists andtransfecting the vector in a packaging cell hereof and allowing forproduction of viral particles.

In one aspect, included is the use of a adenovirus serotype hereof toovercome naturally existing or induced, neutralizing host activitytowards adenoviruses administered in vivo for therapeutic applications.The need for a new serotype is stressed by observations that 1) repeatedsystemic delivery of recombinant Ad5 is unsuccessful due to theformation of high titers of neutralizing antibodies against recombinantAd5 (Schulick et al., 1997), and 2) pre-existing or humoral immunity isalready widespread in the population.

In another aspect, provided is the use of gene delivery vehicles hereofor the use of Ad35 for vaccination purposes. Such use prevents, at leastin part, undesired immune responses of the host. Non-limiting examplesof undesired immune responses include evoking an immune response againstthe gene delivery vehicle or Ad35 and/or boosting an immune responseagainst the gene delivery vehicle or Ad35.

Alternating use may be made of Ad vectors belonging to differentsubgroups. This aspect hereof therefore circumvents the inability torepeat the administration of an adenovirus for gene therapy purposes.

The invention is further described by the use of the followingillustrative Examples.

EXAMPLES Example 1 A High Throughput Assay for the Detection ofNeutralizing Activity in Human Serum

To enable screening of a large amount of human sera for the presence ofneutralizing antibodies against all adenovirus serotypes, an automated96-well assay was developed.

Human Sera

A panel of 100 individuals was selected. Volunteers (50% male, 50%female) were healthy individuals between ages 20 and 60 years old withno restriction for race. All volunteers signed an informed consent form.People professionally involved in adenovirus research were excluded.

Approximately 60 ml blood was drawn in dry tubes. Within two hours aftersampling, the blood was centrifuged at 2500 rpm for 10 minutes.Approximately 30 ml serum was transferred to polypropylene tubes andstored frozen at −20° C. until further use.

Serum was thawed and heat-inactivated at 56° C. for 10 minutes and thenaliquoted to prevent repeated cycles of freeze/thawing. Part was used tomake five steps of twofold dilutions in medium (DMEM, Gibco BRL) in aquantity enough to fill out approximately 70 96-well plates. Aliquots ofundiluted and diluted sera were pipetted in deep well plates (96-wellformat) and, using a programmed platemate, dispensed in 100 μl aliquotsinto 96-well plates. This way the plates were loaded with eightdifferent sera in duplo (100 μl/well) according to the scheme below:

S1/2 S1/4 S1/8 S1/16 S1/32 S5/2 S5/4 S5/8 S5/16 S5/32 — — S1/2 S1/4 S1/8S1/16 S1/32 S5/2 S5/4 S5/8 S5/16 S5/32 — — S2/2 S2/4 S2/8 S2/16 S2/32S6/2 S6/4 S6/8 S6/16 S6/32 — — S2/2 S2/4 S2/8 S2/16 S2/32 S6/2 S6/4 S6/8S6/16 S6/32 — — S3/2 S3/4 S3/8 S3/16 S3/32 S7/2 S7/4 S7/8 S7/16 S7/32 —— S3/2 S3/4 S3/8 S3/16 S3/32 S7/2 S7/4 S7/8 S7/16 S7/32 — — S4/2 S4/4S3/8 S3/16 S3/32 S8/2 S8/4 S8/8 S8/16 S8/32 — — S4/2 S4/4 S3/8 S3/16S3/32 S8/2 S8/4 S8/8 S8/16 S8/32 — —Where S1/2 to S8/2 in columns 1 and 6 represent 1× diluted sera andwhere Sx/4, Sx/8, Sx/16, and Sx/32 are the twofold serial dilutions. Thelast plates also contained four wells filled with 100 μl fetal calfserum as a negative control.

Plates were kept at −20° C. until further use.

Preparation of Human Adenovirus Stocks

Prototypes of all known human adenoviruses were inoculated on T25 flasksseeded with PER.C6 cells (Fallaux et al., 1998) and harvested upon fullCPE. After freeze/thawing 1-2 ml of the crude lysates was used toinoculate a T80 flask with PER.C6 and virus was harvested at full CPE.The timeframe between inoculation and occurrence of CPE as well as theamount of virus needed to re-infect a new culture, differed betweenserotypes. Adenovirus stocks were prepared by freeze/thawing and used toinoculate 3-4 T175 cm² three-layer flasks with PER.C6 cells. Uponoccurrence of CPE, cells were harvested by tapping the flask, pelletedand virus was isolated and purified by a two-step CsCl gradient asfollows. Cell pellets were dissolved in 50 ml 10 mM NaPO₄ buffer (pH7.2) and frozen at −20° C. After thawing at 37° C., 5.6 ml sodiumdeoxycholate (5% w/v) was added. The solution was mixed gently andincubated for 5-15 minutes at 37° C. to completely lyse the cells. Afterhomogenizing the solution, 1875 l 1M MgCl₂ was added. After the additionof 375 l DNAse (10 mg/ml) the solution was incubated for 30 minutes at37° C. Cell debris was removed by centrifugation at 1880×g for 30minutes at RT without brake. The supernatant was subsequently purifiedfrom proteins by extraction with FREON (3×). The cleared supernatant wasloaded on a 1M Tris/HCl buffered cesium chloride block gradient (range:1.2/1.4 g/ml) and centrifuged at 21000 rpm for 2.5 hours at 10° C. Thevirus band was isolated after which a second purification using a 1MTris/HCl buffered continuous gradient of 1.33 g/ml of cesium chloridewas performed. The virus was then centrifuged for 17 hours at 55000 rpmat 10° C. The virus band was isolated and sucrose (50% w/v) was added toa final concentration of 1%. Excess cesium chloride was removed bydialysis (three times 1 hour at RT) in dialysis slides (Slide-a-lizer,cut off 10000 kDa, Pierce, USA) against 1.5 liter PBS supplemented withCaCl₂ (0.9 mM), MgCl₂ (0.5 mM) and an increasing concentration ofsucrose (1, 2, 5%). After dialysis, the virus was removed from theslide-a-lizer after which it was aliquoted in portions of 25 and 100 lupon which the virus was stored at −85° C.

To determine the number of virus particles per milliliter, 50 μl of thevirus batch was run on a high-pressure liquid chromatograph (HPLC) asdescribed by Shabram et al. (1997). Viruses were eluted using a NaClgradient ranging from 0 to 600 mM. As depicted in table I, the NaClconcentration by which the viruses were eluted differed significantlyamong serotypes.

Most human adenoviruses replicated well on PER.C6 cells with a fewexceptions. Adenovirus type 8 and 40 were grown on 911-E4 cells (He etal., 1998). Purified stocks contained between 5×10¹⁰ and 5×10¹² virusparticles/ml (VP/ml; see table I).

Titration of Purified Human Adenovirus Stocks

Adenoviruses were titrated on PER.C6 cells to determine the amount ofvirus necessary to obtain full CPE in five days, the length of theneutralization assay. Hereto, 100 μl medium was dispensed into each wellof 96-well plates. 25 μl of adenovirus stocks pre-diluted 10⁴, 10⁵, 10⁶or 10⁷ times were added to column 2 of a 96-well plate and mixed bypipetting up and down ten times. Then 25 μl was brought from column 2 tocolumn 3 and again mixed. This was repeated until column 11 after which25 μl from column 11 was discarded. This way, serial dilutions in stepsof five were obtained starting off from a pre-diluted stock. Then 3×10⁴PER.C6 cells (ECACC deposit number 96022940) were added in a 100 μlvolume and the plates were incubated at 37° C., 5% CO₂ for five or sixdays. CPE was monitored microscopically. The method of Reed and Muenschwas used to calculate the cell culture-inhibiting dose 50% (CCID50).

In parallel, identical plates were set up that were analyzed using theMTT assay (Promega). In this assay living cells are quantified bycolorimetric staining. Hereto, 20 μl MTT (7.5 mgr/ml in PBS) was addedto the wells and incubated at 37° C., 5% CO₂ for two hours. Thesupernatant was removed and 100 μl of a 20:1 isopropanol/triton-X100solution was added to the wells. The plates were put on a 96-wellsshaker for three to five minutes to solubilize the precipitatedstaining. Absorbance was measured at 540 nm and at 690 nm (background).By this assay, wells with proceeding CPE or full CPE can bedistinguished.

Neutralization Assay

96-well plates with diluted human serum samples were thawed at 37° C.,5% CO₂. Adenovirus stocks diluted to 200 CCID50 per 50 μl were preparedand 50 μl aliquots were added to columns 1-11 of the plates with serum.Plates were incubated for one hour at 37° C., 5% CO₂. Then 50 μl PER.C6cells at 6×10⁵/ml were dispensed in all wells and incubated for one dayat 37° C., 5% CO₂. Supernatant was removed using fresh pipette tips foreach row and 200 μl fresh medium was added to all wells to avoid toxiceffects of the serum. Plates were incubated for another four days at 37°C., 5% CO₂. In addition, parallel control plates were set up in duplowith diluted positive control sera generated in rabbits and specific foreach serotype to be tested in rows A and B and with negative controlserum (FCS) in rows C and D. Also, in each of the rows E-H a titrationwas performed as described above with steps of five times dilutionsstarting with 200 CCID50 of each virus to be tested. On day 5, one ofthe control plates was analyzed microscopically and with the MTT assay.The experimental titer was calculated from the control titration plateobserved microscopically. If CPE was found to be complete, i.e., thefirst dilution in the control titration experiment analyzed by MTT showsclear cell death, all assay plates were processed. If not, the assay wasallowed to proceed for one or more days until full CPE was apparentafter which all plates were processed. In most cases, the assay wasterminated at day 5. For Ad1, 5, 33, 39, 42 and 43 the assay was leftfor six days and for Ad2 for eight days.

A serum sample is regarded as “non-neutralizing” when, at the highestserum concentration, a maximum protection of 40% is seen compared tocontrols without serum.

The results of the analysis of 44 prototype adenoviruses against serumfrom 100 healthy volunteers are shown in FIG. 1. As expected, thepercentage of serum samples that contained neutralizing antibodies toAd2 and Ad5 was very high. This was also true for most of the lowernumbered adenoviruses. Surprisingly, none of the serum samples containedneutralizing antibodies to Ad35. Also, the number of individuals withneutralizing antibody titers to the serotypes 26, 34 and 48 was verylow. Therefore, recombinant E1-deleted adenoviruses based on Ad35 or oneof the other above mentioned serotypes have an important advantagecompared to recombinant vectors based on Ad5 with respect to clearanceof the viruses by neutralizing antibodies.

Also, Ad5-based vectors that have (parts of) the capsid proteinsinvolved in immunogenic response of the host replaced by thecorresponding (parts of) the capsid proteins of Ad35 or one of the otherserotypes will be less, or even not, neutralized by the vast majority ofhuman sera.

As can be seen in Table I, the VP/CCID50 ratio calculated from the virusparticles per ml and the CCID50 obtained for each virus in theexperiments was highly variable, and ranged from 0.4 to 5 log. This isprobably caused by different infection efficiencies of PER.C6 cells andby differences in replication efficiency of the viruses. Furthermore,differences in batch qualities may play a role. A high VP/CCID50 ratiomeans that more viruses were put in the wells to obtain CPE in fivedays. As a consequence, the outcome of the neutralization study might bebiased since more (inactive) virus particles could shield theantibodies. To check whether this phenomenon had taken place, theVP/CCID50 ratio was plotted against the percentage of serum samplesfound positive in the assay (FIG. 2). The graph clearly shows that thereis no negative correlation between the amount of viruses in the assayand neutralization in serum.

Example 2 Generation of Ad5 Plasmid Vectors for the Production ofRecombinant Viruses and Easy Manipulation of Adenoviral Genes

pBr/Ad.Bam-rITR (ECACC Deposit P97082122)

In order to facilitate blunt end cloning of the ITR sequences, wild-typehuman adenovirus type 5 (Ad5) DNA was treated with Klenow enzyme in thepresence of excess dNTPs. After inactivation of the Klenow enzyme andpurification by phenol/chloroform extraction followed by ethanolprecipitation, the DNA was digested with BamHI. This DNA preparation wasused without further purification in a ligation reaction with pBr322derived vector DNA prepared as follows: pBr322 DNA was digested withEcoRV and BamHI, dephosphorylated by treatment with TSAP enzyme (LifeTechnologies) and purified on LMP agarose gel (SeaPlaque GTG). Aftertransformation into competent E. coli DH5 (Life Techn.) and analysis ofampicillin resistant colonies, one clone was selected that showed adigestion pattern as expected for an insert extending from the BamHIsite in Ad5 to the right ITR.

Sequence analysis of the cloning border at the right ITR revealed thatthe most 3′ G residue of the ITR was missing, the remainder of the ITRwas found to be correct. The missing G residue is complemented by theother ITR during replication.

pBr/Ad.Sal-rITR (ECACC Deposit P97082119)

pBr/Ad.Bam-rITR was digested with BamHI and SalI. The vector fragmentincluding the adenovirus insert was isolated in LMP agarose (SeaPlaqueGTG) and ligated to a 4.8 kb SalI-BamHI fragment obtained from wt Ad5DNA and purified with the GENECLEAN II kit (Bio 101, Inc.). One clonewas chosen and the integrity of the Ad5 sequences was determined byrestriction enzyme analysis. Clone pBr/Ad.Sal-rITR contains Ad5sequences from the SalI site at bp 16746 up to and including the rITR(missing the most 3′ G residue).

pBr/Ad.Cla-Bam (ECACC Deposit P97082117)

Wild-type (“wt”) Ad5 DNA was digested with ClaI and BamHI, and the 20.6kb fragment was isolated from gel by electro-elution. pBr322 wasdigested with the same enzymes and purified from agarose gel byGENECLEAN. Both fragments were ligated and transformed into competentDH5. The resulting clone pBr/Ad.Cla-Bam was analyzed by restrictionenzyme digestion and shown to contain an insert with adenovirussequences from bp 919 to 21566.

pBr/Ad.AflII-Bam (ECACC Deposit P97082114)

Clone pBr/Ad.Cla-Bam was linearized with EcoRI (in pBr322) and partiallydigested with AflII. After heat inactivation of AflII for 20 minutes at65° C., the fragment ends were filled in with Klenow enzyme. The DNA wasthen ligated to a blunt double-stranded oligo linker containing a PacIsite (5-AATTGTCTTAATTAACCGCTTAA-3 (SEQ ID NO:1)). This linker was madeby annealing the following two oligonucleotides: 5-AATTGTCTTAATTAACCGC-3(SEQ ID NO:2) and 5-AATTGCGGTTAATTAAGAC-3 (SEQ ID NO:3), followed byblunting with Klenow enzyme. After precipitation of the ligated DNA tochange buffer, the ligations were digested with an excess PacI enzyme toremove concatamers of the oligo. The 22016 bp partial fragmentcontaining Ad5 sequences from bp 3534 up to 21566 and the vectorsequences, was isolated in LMP agarose (SeaPlaque GTG), re-ligated andtransformed into competent DH5. One clone that was found to contain thePacI site and that had retained the large adeno fragment was selectedand sequenced at the 5 end to verify correct insertion of the PacIlinker in the (lost) AflII site.

pBr/Ad.Bam-rITRpac#2 (ECACC Deposit P97082120) and pBr/Ad.Bam-rITRpac#8(ECACC Deposit P97082121)

To allow insertion of a PacI site near the ITR of Ad5 in clonepBr/Ad.Bam-rITR, about 190 nucleotides were removed between the ClaIsite in the pBr322 backbone and the start of the ITR sequences. This wasdone as follows: pBr/Ad.Bam-rITR was digested with ClaI and treated withnuclease Bal31 for varying lengths of time (2 minutes, 5 minutes, 10minutes and 15 minutes). The extent of nucleotide removal was followedby separate reactions on pBr322 DNA (also digested at the ClaI site),using identical buffers and conditions. Bal31 enzyme was inactivated byincubation at 75° C. for 10 minutes, the DNA was precipitated andre-suspended in a smaller volume TE buffer. To ensure blunt ends, DNAswere further treated with T4 DNA polymerase in the presence of excessdNTPs. After digestion of the (control) pBr322 DNA with SalI,satisfactory degradation (˜150 bp) was observed in the samples treatedfor 10 minutes or 15 minutes. The 10 minutes or 15 minutes treatedpBr/Ad.Bam-rITR samples were then ligated to the above described bluntedPacI linkers (See pBr/Ad.AflII-Bam). Ligations were purified byprecipitation, digested with excess PacI and separated from the linkerson an LMP agarose gel. After re-ligation, DNAs were transformed intocompetent DH5 and colonies analyzed. Ten clones were selected thatshowed a deletion of approximately the desired length and these werefurther analyzed by T-track sequencing (T7 sequencing kit, PharmaciaBiotech). Two clones were found with the PacI linker inserted justdownstream of the rITR. After digestion with PacI, clone #2 has 28 bpand clone #8 has 27 bp attached to the ITR.

pWE/Ad.AflII-rITR (ECA CC Deposit P97082116)

Cosmid vector pWE15 (Clontech) was used to clone larger Ad5 inserts.First, a linker containing a unique PacI site was inserted in the EcoRIsites of pWE15 creating pWE.pac. To this end, the double stranded PacIoligo as described for pBr/Ad.AflII-BamHI was used but now with itsEcoRI protruding ends. The following fragments were then isolated byelectro-elution from agarose gel: pWE.pac digested with PacI,pBr/AflII-Bam digested with PacI and BamHI and pBr/Ad.Bam-rITR#2digested with BamHI and PacI. These fragments were ligated together andpackaged using phage packaging extracts (Stratagene) according to themanufacturer's protocol. After infection into host bacteria, colonieswere grown on plates and analyzed for presence of the complete insert.pWE/Ad.AflII-rITR contains all adenovirus type 5 sequences from bp 3534(AflII site) up to and including the right ITR (missing the most 3 Gresidue).

pBr/Ad.lITR-Sal(9.4) (ECACC Deposit P97082115)

Adeno 5 wt DNA was treated with Klenow enzyme in the presence of excessdNTPs and subsequently digested with SalI. Two of the resultingfragments, designated left ITR-Sal(9.4) and Sal(16.7)-right ITR,respectively, were isolated in LMP agarose (Seaplaque GTG). pBr322 DNAwas digested with EcoRV and SalI and treated with phosphatase (LifeTechnologies). The vector fragment was isolated using the GENECLEANmethod (BIO 101, Inc.) and ligated to the Ad5 SalI fragments. Only theligation with the 9.4 kb fragment gave colonies with an insert. Afteranalysis and sequencing of the cloning border a clone was chosen thatcontained the full ITR sequence and extended to the SalI site at bp9462.

pBr/Ad.lITR-Sal(16.7) (ECACC Deposit P97082118)

pBr/Ad.lITR-Sal(9.4) is digested with SalI and dephosphorylated (TSAP,Life Technologies). To extend this clone up to the third SalI site inAd5, pBr/Ad.Cla-Bam was linearized with BamHI and partially digestedwith SalI. A 7.3 kb SalI fragment containing adenovirus sequences from9462-16746 was isolated in LMP agarose gel and ligated to theSalI-digested pBr/Ad.lITR-Sal(9.4) vector fragment.

pWE/Ad.AflII-EcoRI

pWE.pac was digested with ClaI and 5 protruding ends were filled usingKlenow enzyme. The DNA was then digested with PacI and isolated fromagarose gel. pWE/AflII-rITR was digested with EcoRI and after treatmentwith Klenow enzyme digested with PacI. The large 24 kb fragmentcontaining the adenoviral sequences was isolated from agarose gel andligated to the ClaI-digested and blunted pWE.pac vector using theLigation Express™ kit from Clontech. After transformation ofUltracompetent XL10-Gold cells from Stratagene, clones were identifiedthat contained the expected insert. pWE/AflII-EcoRI contains Ad5sequences from bp 3534-27336.

Generation of p WE/Ad.AflII-rITRsp

The 3 ITR in the vector pWE/Ad.AflII-rITR does not include the terminalG-nucleotide. Furthermore, the PacI site is located almost 30 bp fromthe right ITR. Both these characteristics may decrease the efficiency ofvirus generation due to inefficient initiation of replication at the 3ITR. Note that during virus generation, the left ITR in the adapterplasmid is intact and enables replication of the virus DNA afterhomologous recombination.

To improve the efficiency of initiation of replication at the 3 ITR, thepWE/Ad.AflII-rITR was modified as follows: constructpBr/Ad.Bam-rITRpac#2 was first digested with PacI and then partiallydigested with AvrII and the 17.8 kb vector containing fragment wasisolated and dephosphorylated using SAP enzyme (Boehringer Mannheim).This fragment lacks the adenovirus sequences from nucleotide 35464 tothe 3 ITR. Using DNA from pWE/Ad.AflII-rITR as template and the primersITR-EPH: 5-CGG AAT TCT TAA TTA AGT TAA CAT CAT CAA TAA TAT ACC-3 (SEQ IDNO:4) and Ad101: 5-TGA TTC ACA TCG GTC AGT GC-3 (SEQ ID NO:5).

A 630 bp PCR fragment was generated corresponding to the 3 Ad5sequences. This PCR fragment was subsequently cloned in the vectorpCR2.1 (Invitrogen) and clones containing the PCR fragment were isolatedand sequenced to check correct DNA amplification. The PCR clone was thendigested with PacI and AvrII and the 0.5 kb adeno insert was ligated tothe PacI/partial AvrII-digested pBr/Ad.Bam-rITRpac#2 fragment generatingpBr/Ad.Bam-rITRsp. Next, this construct was used to generate a cosmidclone (as previously described herein) that has an insert correspondingto the adenovirus sequences 3534 to 35938. This clone was designatedpWE/AflII-rITRsp.

Generation of pWE/Ad.AflII-rITRΔE2A:

Deletion of the E2A coding sequences from pWE/Ad.AflII-rITR (ECACCdeposit P97082116) has been accomplished as follows. The adenoviralsequences flanking the E2A coding region at the left and the right sitewere amplified from the plasmid pBr/Ad.Sal.rITR (ECACC depositP97082119) in a PCR reaction with the Expand PCR system (Boehringer)according to the manufacturer's protocol. The following primers wereused:

Right flanking sequences (corresponding Ad5 nucleotides 24033 to 25180):E2A.SnaBI: 5-GGC GTA CGT AGC CCT GTC GAA AG-3 (SEQ ID NO:6) andE2A.DBP-start: 5-CCA ATG CAT TCG AAG TAC TTC CTT CTC CTA TAG GC-3 (SEQID NO:7). The amplified DNA fragment was digested with SnaBI and NsiI(NsiI site is generated in the primer E2A.DBP-start, underlined).

Left flanking sequences (corresponding Ad5 nucleotides 21557 to 22442):E2A.DBP-stop: 5-CCA ATG CAT ACG GCG CAG ACG G-3 (SEQ ID NO:8) andE2A.BamHI: 5-GAG GTG GAT CCC ATG GAC GAG-3 (SEQ ID NO:9).

The amplified DNA was digested with BamHI and NsiI (NsiI site isgenerated in the primer E2A.DBP-stop, underlined). Subsequently, thedigested DNA fragments were ligated into SnaBI/BamHI-digestedpBr/Ad.Sal-rITR. Sequencing confirmed the exact replacement of the DBPcoding region with a unique NsiI site in plasmid pBr/Ad.Sal-rITR E2A.The unique NsiI site can be used to introduce an expression cassette fora gene to be transduced by the recombinant vector.

The deletion of the E2A coding sequences was performed such that thesplice acceptor sites of the 100K encoding L4-gene at position 24048 inthe top strand was left intact. In addition, the poly-adenylationsignals of the original E2A-RNA and L3-RNAs at the left hand site of theE2A coding sequences were left intact. This ensures proper expression ofthe L3-genes and the gene encoding the 100K L4-protein during theadenovirus life cycle.

Next, the plasmid pWE/Ad.AflII-rITR E2A was generated. The plasmidpBr/Ad.Sal-rITR E2A was digested with BamHI and SpeI. The 3.9 Kbfragment in which the unique NsiI site replaced the E2A coding regionwas isolated. The pWE/Ad.AflII-rITR was digested with BamHI and SpeI.The 35 Kb DNA fragment, from which the BamHI/SpeI fragment containingthe E2A coding sequence was removed, was isolated. The fragments wereligated and packaged using phage-packaging extracts according to themanufacturer protocol (Stratagene), yielding the plasmidpWE/Ad.AflII-rITR E2A.

This cosmid clone can be used to generate adenoviral vectors that aredeleted for E2A by co-transfection of PacI-digested DNA together withdigested adapter plasmids onto packaging cells that express functionalE2A gene product.

Construction of Adapter Plasmids

The absence of sequence overlap between the recombinant adenovirus andE1 sequences in the packaging cell line is essential for safe, RCA-freegeneration and propagation of new recombinant viruses. The adapterplasmid pMLPI.TK (described in U.S. Pat. No. 5,994,128 to Bout et al.)is an example of an adapter plasmid designed for use hereof incombination with the improved packaging cell lines hereof. This plasmidwas used as the starting material to make a new vector in which nucleicacid molecules comprising specific promoter and gene sequences can beeasily exchanged.

First, a PCR fragment was generated from pZip Mo+PyF101(N⁻) template DNA(described in PCT/NL96/00195) with the following primers: LTR-1: 5-CTGTAC GTA CCA GTG CAC TGG CCT AGG CAT GGA AAA ATA CAT AAC TG-3 (SEQ IDNO:10) and LTR-2: 5-GCG GAT CCT TCG AAC CAT GGT AAG CTT GGT ACC GCT AGCGTT AAC CGG GCG ACT CAG TCA ATC G-3 (SEQ ID NO:11). Pwo DNA polymerase(Boehringer Mannheim) was used according to manufacturer's protocol withthe following temperature cycles: once five minutes at 95° C.; threeminutes at 55° C.; and one minute at 72° C., and 30 cycles of one minuteat 95° C., one minute at 60° C., one minute at 72° C., followed by onceten minutes at 72° C. The PCR product was then digested with BamHI andligated into pMLP10 (Levrero et al., 1991) vector digested with PvuIIand BamHI, thereby generating vector pLTR10. This vector containsadenoviral sequences from bp 1 up to bp 454 followed by a promoterconsisting of a part of the Mo-MuLV LTR having its wild-type enhancersequences replaced by the enhancer from a mutant polyoma virus (PyP101).The promoter fragment was designated L420. Next, the coding region ofthe murine HSA gene was inserted. pLTR10 was digested with BstBIfollowed by Klenow treatment and digestion with NcoI. The HSA gene wasobtained by PCR amplification on pUC18-HSA (Kay et al., 1990) using thefollowing primers: HSA1, 5-GCG CCA CCA TGG GCA GAG CGA TGG TGG C-3 (SEQID NO:12) and HSA2, 5-GTT AGA TCT AAG CTT GTC GAC ATC GAT CTA CTA ACAGTA GAG ATG TAG AA-3 (SEQ ID NO:13). The 269 bp amplified fragment wassubcloned in a shuttle vector using the NcoI and BglII sites. Sequencingconfirmed incorporation of the correct coding sequence of the HSA gene,but with an extra TAG insertion directly following the TAG stop codon.The coding region of the HSA gene, including the TAG duplication wasthen excised as a NcoI(sticky)-SalI(blunt) fragment and cloned into the3.5 kb NcoI(sticky)/BstBI(blunt) fragment from pLTR10, resulting inpLTR-HSA10.

Finally, pLTR-HSA10 was digested with EcoRI and BamHI after which thefragment containing the left ITR, packaging signal, L420 promoter andHSA gene was inserted into vector pMLPI.TK digested with the sameenzymes and thereby replacing the promoter and gene sequences. Thisresulted in the new adapter plasmid pAd/L420-HSA that containsconvenient recognition sites for various restriction enzymes around thepromoter and gene sequences. SnaBI and AvrII can be combined with HpaI,NheI, KpnI, HindIII to exchange promoter sequences, while the lattersites can be combined with the ClaI or BamHI sites 3 from HSA codingregion to replace genes in this construct.

Replacing the promoter, gene and poly-A sequences in pAd/L420-HSA withthe CMV promoter, a multiple cloning site, an intron and a poly-A signalmade another adapter plasmid that was designed to allow easy exchange ofnucleic acid molecules. For this purpose, pAd/L420-HSA was digested withAvrII and BglII followed by treatment with Klenow to obtain blunt ends.The 5.1 kb fragment with pBr322 vector and adenoviral sequences wasisolated and ligated to a blunt 1570 bp fragment from pcDNA1/amp(Invitrogen) obtained by digestion with HhaI and AvrII followed bytreatment with T4 DNA polymerase. This adapter plasmid was designatedpAd5/CLIP.

To enable removal of vector sequences from the left ITR in pAd5/Clip,this plasmid was partially digested with EcoRI and the linear fragmentwas isolated. An oligo of the sequence 5 TTAAGTCGAC-3 (SEQ ID NO:14) wasannealed to itself resulting in a linker with a SalI site and EcoRIoverhang. The linker was ligated to the partially digested pAd5/Clipvector and clones were selected that had the linker inserted in theEcoRI site 23 bp upstream of the left adenovirus ITR in pAd5/Clipresulting in pAd5/Clipsal. Likewise, the EcoRI site in pAd5/Clip hasbeen changed to a PacI site by insertion of a linker of the sequence5-AATTGTCTTAATTAACCGCAATT-3 (SEQ ID NO:15). The pAd5/Clip vector waspartially digested with EcoRI, dephosphorylated and ligated to the PacIlinker with EcoRI overhang. The ligation mixture was digested with PacIto remove concatamers, isolated from agarose gel and religated. Theresulting vector was designated pAd5/Clippac. These changes enable moreflexibility to liberate the left ITR from the plasmid vector sequences.

The vector pAd5/L420-HSA was also modified to create a SalI or PacI siteupstream of the left ITR. Hereto pAd5/L420-HSA was digested with EcoRIand ligated to the previously herein described PacI linker. The ligationmixture was digested with PacI and religated after isolation of thelinear DNA from agarose gel to remove concatamerized linkers. Thisresulted in adapter plasmid pAd5/L420-HSApac. This construct was used togenerate pAd5/L420-HSAsal as follows: pAd5/L420-HSApac was digested withScaI and BsrGI and the vector fragment was ligated to the 0.3 kbfragment isolated after digestion of pAd5/Clipsal with the same enzymes.

Generation of Adapter Plasmids pAdMire and pAdApt

To create an adapter plasmid that only contains a polylinker sequenceand no promoter or polyA sequences, pAd5/L420-HSApac was digested withAvrII and BglII. The vector fragment was ligated to a linkeroligonucleotide digested with the same restriction enzymes. Annealingoligos of the following sequence made the linker: PLL-1: 5-GCC ATC CCTAGG AAG CTT GGT ACC GGT GAA TTC GCT AGC GTT AAC GGA TCC TCT AGA CGA GATCTG G-3 (SEQ ID NO:16) and PLL-2: 5-CCA GAT CTC GTC TAG AGG ATC CGT TAACGC TAG CGA ATT CAC CGG TAC CAA GCT TCC TAG GGA TGG C-3 (SEQ ID NO:17).The annealed linkers were digested with AvrII and BglII and separatedfrom small ends by column purification (Qiaquick nucleotide removal kit)according to manufacturer's recommendations. The linker was then ligatedto the AvrII/BglII-digested pAd5/L420-HSApac fragment. A clone,designated AdMire, was selected that had the linker incorporated and wassequenced to check the integrity of the insert.

Adapter Plasmid AdMire Enables Easy Insertion of Complete ExpressionCassettes

An adapter plasmid containing the human CMV promoter that mediates highexpression levels in human cells was constructed as follows:pAd5/L420-HSApac was digested with AvrII and 5 protruding ends werefilled in using Klenow enzyme. A second digestion with HindIII resultedin removal of the L420 promoter sequences. The vector fragment wasisolated and ligated to a PCR fragment containing the CMV promotersequence. This PCR fragment was obtained after amplification of CMVsequences from pCMVLacI (Stratagene) with the following primers:CMVplus: 5-GATCGGTACCACTGCAGTGGTCAATATTGGCCATTAGCC-3 (SEQ ID NO:18) andCMVminA: 5-GATCAAGCTTCCAATGCACCGTTCCCGGC-3 (SEQ ID NO:19).

The PCR fragment was first digested with PstI (underlined in CMVplus)after which the 3-protruding ends were removed by treatment with T4 DNApolymerase. Then the DNA was digested with HindIII (underlined inCMVminA) and ligated into the herein described pAd5/L420-HSApac vectorfragment digested with AvrII and HindIII. The resulting plasmid wasdesignated pAd5/CMV-HSApac. This plasmid was then digested with HindIIIand BamHI and the vector fragment was isolated and ligated to thepolylinker sequence obtained after digestion of AdMire with HindIII andBglII. The resulting plasmid was designated pAdApt. Adapter plasmidpAdApt contains nucleotides −735 to +95 of the human CMV promoter(Boshart et al., 1985). A second version of this adapter plasmidcontaining a SalI site in place of the PacI site upstream of the leftITR was made by inserting the 0.7 kb ScaI-BsrGI fragment frompAd5/Clipsal into pAdApt digested with ScaI and partially digested withBsrGI. This clone was designated pAdApt.sal.

Generation of Recombinant Adenoviruses Based on Ad5

RCA-free recombinant adenoviruses can be generated very efficientlyusing the herein described adapter plasmids and the pWe/Ad.AflII-rITR orpWE/Ad.AflII-rITrsp constructs. Generally, the adapter plasmidcontaining the desired transgene in the desired expression cassette isdigested with suitable enzymes to liberate the insert from vectorsequences at the 3 and/or at the 5 end. The adenoviral complementationplasmids pWE/Ad.AflII-rITR or pWE/Ad.AflII-rITRsp are digested with PacIto liberate the adeno sequences from the vector plasmids. As anon-limiting example, the generation of AdApt-LacZ is described. Adapterplasmid pAdApt-LacZ was generated as follows. The E. coli LacZ gene wasamplified from the plasmid pMLP.nlsLacZ (EP 95-202 213) by PCR with theprimers 5-GGGGTGGCCAGGGTACCTCTAGGCTTTTGCAA-3 (SEQ ID NO:20) and5-GGGGGGATCCATAAACAAGTTCAGAATCC-3 (SEQ ID NO:21). The PCR reaction wasperformed with Ex Taq (Takara) according to the suppliers protocol atthe following amplification program: five minutes 94° C., one cycle; 45seconds 94° C. and 30 seconds 60° C. and two minutes 72° C., fivecycles; 45 seconds 94° C. and 30 seconds 65° C. and two minutes 72° C.,25 cycles; ten minutes 72; 45 seconds 94° C. and 30 seconds 60° C. andtwo minutes 72° C., five cycles, I cycle. The PCR product wassubsequently digested with KpnI and BamHI and the digested DNA fragmentwas ligated into KpnI/BamHI-digested pcDNA3 (Invitrogen), giving rise topcDNA3.nlsLacZ. Construct pcDNA3.nlsLacZ was then digested with KpnI andBamHI and the 3 kb LacZ fragment was isolated from gel using theGENECLEAN spin kit (Bio 101, Inc.). pAdApt was also digested with KpnIand BamHI and the linear vector fragment was isolated from gel as above.Both isolated fragments were ligated and one clone containing the LacZinsert was selected. Construct pAdApt-LacZ was digested with SalI,purified by the GENECLEAN spin kit and subsequently digested with PacI.pWE/Ad.AflII-rITRsp was digested with PacI. Both digestion mixtures weretreated for 30 minutes by 65° C. to inactivate the enzymes. Samples wereput on gel to estimate the concentration. 2.5×10⁶ PER.C6 cells wereseeded in T25 flasks in DMEM with 10% FCS and 10 mM MgCl. The next day,four microgram of each plasmid was transfected into PER.C6 cells usinglipofectamine transfection reagents (Life Technologies Inc.) accordingto instructions of the manufacturer. The next day, the medium wasreplaced by fresh culture medium and cells were further cultured at 37°C., 10% CO₂. Again, one day later, cells were trypsinized, seeded intoT80 flasks and cultured at 37° C., 10% CO₂. Full CPE was obtained 6 daysafter seeding in the T80 flask. Cells were harvested in the medium andsubjected to one freeze/thaw cycle. The crude lysate obtained this waywas used to plaque-purify the mixture of viruses. Ten plaques werepicked, expanded in a 24-well plate and tested for LacZ expressionfollowing infection of A549 cells. Viruses from all ten plaquesexpressed LacZ.

Example 3 Generation of Chimeric Recombinant Adenoviruses Generation ofHexon Chimeric Ad5-Based Adenoviruses

Neutralizing antibodies in human serum are mainly directed to the hexonprotein and to a lesser extend to the penton protein. Hexon proteinsfrom different serotypes show highly variable regions present in loopsthat are predicted to be exposed at the outside of the virus (Athappillyet al., 1994; J. Mol. Biol. 242, 430-455). Most type-specific epitopeshave been mapped to these highly variable regions (Toogood et al., 1989;J. Gen Virol. 70, 3203-3214). Thus, replacement of (part of) the hexonsequences with corresponding sequences from a different serotype is aneffective strategy to circumvent (pre-existing) neutralizing antibodiesto Ad5. Hexon coding sequences of Ad5 are located between nucleotides18841 and 21697.

To facilitate easy exchange of hexon coding sequences from alternativeadenovirus serotypes into the Ad5 backbone, first a shuttle vector wasgenerated. This sub-clone, coded pBr/Ad.Eco-PmeI, was generated by firstdigesting plasmid pBr322 with EcoRI and EcoRV and inserting the 14 kbPmeI-EcoRI fragment from pWE/Ad.AflII-Eco. In this shuttle vector adeletion was made of a 1430 bp SanDI fragment by digestion with SanDIand re-ligation to give pBr/Ad.Eco-PmeI SanDI. The removed fragmentcontains unique SpeI and MunI sites. From pBr/Ad.Eco-PmeI SanDI the Ad5DNA encoding hexon was deleted. Hereto, the hexon flanking sequenceswere PCR amplified and linked together thereby generating uniquerestriction sites replacing the hexon coding region. For these PCRreactions four different oligonucleotides were required: hex1-hex4:hex1: 5-CCT GGT GCT GCC AAC AGC-3 (SEQ. I.D. NO. 22), hex2: 5-CCG GATCCA CTA GTG GAA AGC GGG CGC GCG-3 (SEQ ID NO:23), hex3: 5-CCG GAT CCAATT GAG AAG CAA GCA ACA TCA ACA AC-3 (SEQ ID NO:24), and hex4: 5-GAG AAGGGC ATG GAG GCT G-3 (SEQ ID NO:25).

The amplified DNA product of ±1100 bp obtained with oligonucleotideshex1 and hex2 was digested with BamHI and FseI. The amplified DNAproduct of ±1600 bp obtained with oligonucleotides hex3 and hex4 wasdigested with BamHI and SbfI. These digested PCR fragments weresubsequently purified from agarose gel and in a tri-part ligationreaction using T4 ligase enzyme linked to pBr/Ad.Eco-PmeI SanDI digestedwith FseI and SbfI. The resulting construct was coded pBr/Ad.Eco-PmeHexon. This construct was sequenced in part to confirm the correctnucleotide sequence and the presence of unique restriction sites MunIand SpeI.

pBr/Ad.Eco-Pme Hexon serves as a shuttle vector to introduceheterologous hexon sequences amplified from virus DNA from differentserotypes using primers that introduce the unique restriction sites MunIand SpeI at the 5 and 3 ends of the hexon sequences respectively. Togenerate Ad5-based vectors that contain hexon sequences from theserotypes to which healthy individuals have no, or very low, titers ofNAB the hexon sequences of Ad35, Ad34, Ad26 and Ad48 were amplifiedusing the following primers: Hex-up2:5-GACTAGTCAAGATGGCYACCCCHTCGATGATG-3 (SEQ ID NO:26) (where Y can be a Cor T and H can be an A, T or C as both are degenerate oligo nucleotides)and Hex-do2: 5-GCTGGCCAATTGTTATGTKGTKGCGTTRCCGGC-3 (SEQ ID NO:27) (whereK can be a T or G and R can be an A or G as both are degenerate oligonucleotides).

These primers were designed using the sequences of published hexoncoding regions (for example hexon sequences of Ad2, Ad3, Ad4, Ad5, Ad7,Ad16, Ad40 and Ad41 can be obtained at Genbank). Degenerated nucleotideswere incorporated at positions that show variation between serotypes.

PCR products were digested with SpeI and MunI and cloned into thepBr/Ad.Eco-Pme Hexon construct digested with the same enzymes.

The hexon modified sequences were subsequently introduced in theconstruct pWE/Ad.AflII-rITR by exchange of the AscI fragment generatingpWE/Ad.AflII-rITRHexXX where XX stands for the serotype used to amplifyhexon sequences.

The pWE/Ad.AflII-rITRHexXX constructs were then used to make viruses inthe same manner as previously described herein for Ad5 recombinantviruses.

Generation of Penton Chimeric Ad5-Based Recombinant Viruses

The adenovirus type 5 penton gene is located between sequences 14156 and15869. Penton base is the adenovirus capsid protein that mediatesinternalization of the virus into the target cell. At least someserotypes (type C and B) have been shown to achieve this by interactionof an RGD sequence in penton with integrins on the cell surface.However, type F adenoviruses do not have an RGD sequence and for mostviruses of the A and D group the penton sequence is not known.Therefore, the penton may be involved in target cell specificity.Furthermore, as a capsid protein, the penton protein is involved in theimmunogenicity of the adenovirus (Gahery-Segard et al., 1998).Therefore, replacement of Ad5 penton sequences with penton sequencesfrom serotypes to which no or low titers of NAB exist in addition toreplacement of the hexon sequences will prevent clearance of theadenoviral vector more efficiently than replacement of hexon alone.Replacement of penton sequences may also affect infection specificity.

To be able to introduce heterologous penton sequences in Ad5 we made useof the plasmid-based system described above. First, a shuttle vector forpenton sequences was made by insertion of the 7.2 kb NheI-EcoRV fragmentfrom construct pWE/Ad.AflII-EcoRI into pBr322 digested with the sameenzymes. The resulting vector was designated pBr/XN. From this plasmid,Ad5 penton sequences were deleted and replaced by unique restrictionsites that were then used to introduce new penton sequences from otherserotypes. Hereto, the left flanking sequences of penton in pBr/XN werePCR amplified using the following primers: DP5-F: 5-CTG TTG CTG CTG CTAATA GC-3 (SEQ ID NO:28) and DP5-R: 5-CGC GGA TCC TGT ACA ACT AAG GGG AATACA AG-3 (SEQ ID NO:29).

DP5-R has a BamHI site (underlined) for ligation to the right flankingsequence and also introduces a unique BsrGI site (bold face) at the5-end of the former Ad5 penton region. The right flanking sequence wasamplified using: DP3-F: 5-CGC GGA TCC CTT AAG GCA AGC ATG TCC ATC CTT-3(SEQ ID NO:30) and DP3-3R: 5-AAA ACA CGT TTT ACG CGT CGA CCT TTC-3 (SEQID NO:31). DP3-F has a BamHI site (underlined) for ligation to the leftflanking sequence and also introduces a unique AflII site (bold face) atthe 3 end of the former Ad5 penton region.

The two resulting PCR fragments were digested with BamHI and ligatedtogether. Then this ligation mixture was digested with AvrII and BglII.pBr/XN was also digested with AvrII and BglII and the vector fragmentwas ligated to the digested ligated PCR fragments. The resulting clonewas designated pBr/Ad. penton. Penton coding sequences from Ad35, Ad34,Ad26 and Ad48 were PCR amplified such that the 5 and 3 ends containedthe BsrGI and AflII sites respectively. Hereto, the following primerswere used:

For Ad34 and Ad35: P3-for: 5-GCT CGA TGT ACA ATG AGG AGA CGA GCC GTGCTA-3 (SEQ ID NO:32) and P3-rev: 5-GCT CGA CTT AAG TTA GAA AGT GCG GCTTGA AAG-3 (SEQ ID NO:33).

For Ad26 and Ad48: P17F: 5-GCT CGA TGT ACA ATG AGG CGT GCG GTG GTG TCTTC-3 (SEQ ID NO:34) and P17R: 5-GCT CGA CTT AAG TTA GAA GGT GCG ACT GGAAAG C-3 (SEQ ID NO:35).

Amplified PCR products were digested with BfrI and BsrGI and cloned intopBr/Ad. penton digested with the same enzymes. Introduction of theseheterologous penton sequences into the pBr/Ad. penton generatedconstructs designated pBr/Ad.pentonXX, wherein XX represents the numberof the serotype corresponding to the serotype used to amplify theinserted penton sequences. Subsequently, the new penton sequences wereintroduced in the pWE/Ad.AfllII-rITR vector having a modified hexon. Forexample, penton sequences from Ad35 were introduced in the constructpWE/Ad.AflII-rITRHex35 by exchange of the common FseI fragment. Othercombinations of penton and hexon sequences were also made. Viruses withmodified hexon and penton sequences were made as described above usingcotransfection with an adapter plasmid on PER.C6 cells. In addition,penton sequences were introduced in the pWE/Ad.AflII-rITR construct. Thelatter constructs contain only a modified penton, and viruses generatedfrom these constructs will be used to study the contribution of pentonsequences to the neutralization of adenoviruses and also for analysis ofpossible changes in infection efficiency and specificity.

Generation of Fiber Chimeric Ad5-Based Viruses

Adenovirus infection is mediated by two capsid proteins fiber andpenton. Binding of the virus to the cells is achieved by interaction ofthe protruding fiber protein with a receptor on the cell surface.Internalization then takes place after interaction of the penton proteinwith integrins on the cell surface. At least some adenovirus fromsubgroups C and B have been shown to use a different receptor for cellbinding and, therefore, have different infection efficiencies ondifferent cell types. Thus, it is possible to change the infectionspectrum of adenoviruses by changing the fiber in the capsid. The fibercoding sequence of Ad5 is located between nucleotides 31042 and 32787.To remove the Ad5 DNA encoding fiber, we started with constructpBr/Ad.Bam-rITR. First, an NdeI site was removed from this construct.For this purpose, pBr322 plasmid DNA was digested with NdeI. Afterwhich, protruding ends were filled using Klenow enzyme. This pBr322plasmid was then re-ligated, digested with NdeI, and transformed into E.coli DH5. The obtained pBr/NdeI plasmid was digested with ScaI and SalIand the resulting 3198 bp vector fragment was ligated to the 15349 bpScaI-SalI fragment derived from pBr/Ad.BamrITR, resulting in plasmidpBr/Ad.Bam-rITR NdeI which hence contained a unique NdeI site. Next, aPCR was performed with oligonucleotides NY-up: 5-CGA CAT ATG TAG ATG CATTAG TTT GTG TTA TGT TTC AAC GTG-3 (SEQ ID NO:36) and NY-down: 5-GGA GACCAC TGC CAT GTT-3 (SEQ ID NO:37).

During amplification, both an NdeI (bold face) and an NsiI restrictionsite (underlined) were introduced to facilitate cloning of the amplifiedfiber DNAs. Amplification consisted of 25 cycles of each 45 seconds at94° C., one minute at 60° C., and 45 seconds at 72° C. The PCR reactioncontained 25 pmol of oligonucleotides NY-up or NY-down, 2 mM dNTP, PCRbuffer with 1.5 mM MgCl₂, and 1 unit of Elongase heat stable polymerase(Gibco, The Netherlands). One-tenth of the PCR product was run on anagarose gel that demonstrated that the expected DNA fragment of ±2200 bpwas amplified. This PCR fragment was subsequently purified usingGENECLEAN kit system (Bio101 Inc.). Then, both the constructpBr/Ad.Bam-rITR NdeI, as well as the PCR product, were digested withrestriction enzymes NdeI and SbfI. The PCR fragment was subsequentlycloned using T4 ligase enzyme into the NdeI- and SbfI-digestedpBr/Ad.Bam-rITR NdeI, generating pBr/Ad.BamR Fib.

This plasmid allows insertion of any PCR-amplified fiber sequencethrough the unique NdeI and NsiI sites that are inserted in place of theremoved fiber sequence. Viruses can be generated by a double homologousrecombination in packaging cells described in U.S. Pat. No. 5,994,128 toBout et al. using an adapter plasmid, construct pBr/Ad.AflII-EcoRIdigested with PacI and EcoRI and a pBr/Ad.BamR Fib construct in whichheterologous fiber sequences have been inserted. To increase theefficiency of virus generation, the construct pBr/Ad.BamR Fib wasmodified to generate a PacI site flanking the right ITR. Hereto,pBr/Ad.BamR Fib was digested with AvrII and the 5 kb adenovirus fragmentwas isolated and introduced into the vector pBr/Ad.Bam-rITR.pac#8described above replacing the corresponding AvrII fragment. Theresulting construct was designated pBr/Ad.BamR Fib.pac.

Once a heterologous fiber sequence is introduced in pBr/Ad.BamR Fib.pac,the fiber-modified right hand adenovirus clone is introduced into alarge cosmid clone as previously described herein for pWE/Ad.AflII-rITR.Such a large cosmid clone allows generation of adenovirus by only onehomologous recombination. Ad5-based viruses with modified fibers havebeen made and described (see, European Patent Appln. Nos. 98204482.8 and99200624.7). In addition, hexon and penton sequences from serotypes fromthis invention are combined with the desired fiber sequences to generateviruses that infect the target cell of choice very efficiently. Forexample, smooth muscle cells, endothelial cells or synoviocytes (allfrom human origin) are very well infected with Ad5-based viruses with afiber from subgroup B viruses, especially Ad16.

The foregoing examples in which specific sequences can be deleted fromthe Ad5 backbone in the plasmids and replaced by corresponding sequencesfrom other serotypes demonstrate the flexibility of the system. It isevident that by the methods described herein, any combination of capsidgene from different serotypes can be made. Thus, chimeric recombinantAd5-based adenoviruses are designed with desired hexon and pentonsequences making the virus less sensitive for neutralization and withdesired fiber sequences allowing efficient infection in specific targettissues.

Example 4 Construction of a Plasmid-Based System to Generate Ad35Recombinant Viruses

Partial restriction maps of Ad35 have been published previously(Valderrama-Leon et al., 1985; Kang et al., 1989; Li et al., 1991). Anexample of a functional plasmid-based system to generate recombinantadenoviruses based on Ad35 consists of the following elements:

1. An adapter plasmid comprising a left ITR and packaging sequencesderived from Ad35 and at least one restriction site for insertion of aheterologous expression cassette and lacking E1 sequences. Furthermore,the adapter plasmid contains Ad35 sequences 3′ from the E1B codingregion including the pIX promoter and coding sequences sufficient tomediate homologous recombination of the adapter plasmid with a secondnucleotide.

2. A second nucleotide comprising sequences homologous to the adapterplasmid and Ad35 sequences necessary for the replication and packagingof the recombinant virus, that is, early, intermediate and late genesthat are not present in the packaging cell.

3. A packaging cell providing at least functional E1 proteins andproteins capable of complementing the E1 function of Ad35.

Ad35 DNA was isolated from a purified virus batch as follows. To 100 lof virus stock (Ad35: 3.26×10¹² VP/ml), 10 l 10×DNAse buffer (130 mMTris-HCl pH7.5; 1.2 M CaCl₂; 50 mM MgCl₂) was added. After addition of10 l 10 mgr/ml DNAse I (Roche Diagnostics), the mixture was incubatedfor one hour at 37° C. Following addition of 2.5 l 0.5M EDTA, 3.2 l 20%SDS and 1.5 l ProteinaseK (Roche Diagnostics; 20 mgr/ml), samples wereincubated at 50° C. for one hour. Next, the viral DNA was isolated usingthe GENECLEAN spin kit (Bio101 Inc.) according to the manufacturer'sinstructions. DNA was eluted from the spin column with 25 l sterileMilliQ water.

In the following, sizes of DNA fragments and fragment numbering will beused according to Kang et al. (1989). Ad35 DNA was digested with EcoRIand the three fragments (approximately 22.3 (A), 7.3 (B) and 6 kb (C))were isolated from gel using the GENECLEAN kit (Bio101, Inc.). pBr322was digested with EcoRI or with EcoRI and EcoRV and digested fragmentswere isolated from gel and dephosphorylated with Tsap enzyme (GibcoBRL). Next, the 6 kb Ad35 C fragment was ligated to the pBr322xEcoRIfragment and the ITR-containing Ad35 fragment (EcoRI-B) was ligated tothe pBr322xEcoRI/EcoRV fragment. Ligations were incubated at 16° C.overnight and transformed into DH5 competent bacteria (Life Techn.).Minipreps of obtained colonies were analyzed for correct insertion ofthe Ad35 fragments by restriction analysis. Both the 6 kb and the 7.3 kbAd35 fragments were found to be correctly inserted in pBr322. The 6 kbfragment was isolated in both orientations pBr/Ad35-Eco6.0⁺ andpBr/Ad35-Eco6.0⁻, whereby the + stands for 5 to 3 orientation relativeto pBr322. The clone with the 7.3 kb Ad35 B insert, designatedpBr/Ad35-Eco7.3 was partially sequenced to check correct ligation of the3 ITR. It was found that the ITR had at least the sequence 5-CATCATCAAT. . . -3 found in SEQ ID NO:40 in the lower strand. Then pBr/Ad35-Eco7.3was extended to the 5 end by insertion of the 6 kb Ad35 fragment.Hereto, pBr/Ad35-Eco7.3 was digested with EcoRI and dephosphorylated.The fragment was isolated from gel and ligated to the 6 kb Ad35 EcoRIfragment. After transformation clones were tested for correctorientation of the insert and one clone was selected, designatedpBr/Ad35-Eco13.3.

This clone was then extended with the ˜5.4 kb SalI D fragment obtainedafter digestion of wt Ad35 with SalI. Hereto, the SalI site in thepBr322 backbone was removed by partial digestion of pBr/Ad35-Eco13.3with SalI, filling in of the sticky ends by Klenow treatment andre-ligation. One clone was selected containing a single SalI site in theadenoviral insert. This clone, pBr sal/Ad35-Eco13.3, was then linearizedwith AatII, which is present in the pBr322 backbone and ligated to aSalI linker with AatII complementary ends. The DNA was then digestedwith excess SalI and the linear fragment was isolated and ligated to the5.4 kb SalI-D fragment from Ad35. One clone was selected that containsthe SalI fragment inserted in the correct orientation inpBr/Ad35-Eco13.3. The resulting clone, pBr/Ad35.Sal2-rITR contained the3 ˜17 kb of Ad35 including the right ITR. To enable liberation of theright ITR from the vector sequences at the time of virus generation, aNotI site flanking the right ITR was introduced by PCR.

The Ad35 EcoRI-A fragment of 22.3 kb was also cloned inpBr322xEcoRI/EcoRV. One clone, designated pBr/Ad35-EcoA3, was selectedthat apparently had a deletion of approximately 7 kb of the 5 end. Itdid contain the SalI site at 9.4 kb in Ad35 wt DNA and approximately 1.5kb of sequences upstream. Using this SalI site and the unique NdeI sitein the pBr322 backbone, this clone is extended to the 5 end by insertionof an approximately 5 kb Ad35 fragment 5 from the first SalI in Ad35 insuch a way that a NotI restriction site was created at the 5 end of theAd35 by insertion of a linker. This clone, designated pBr/Ad35.pIX-EcoA,does not contain the left end sequences (ITR, packaging sequences andE1) and at the 3 end it has approximately 3.5 kb overlap with clonepBr/Ad35.Sal2-rITR.

To create an adapter plasmid, Ad35 was digested with SalI and the leftend B fragment of ˜9.4 kb was isolated. pBr322 was digested with EcoRVand SalI, isolated from gel and dephosphorylated with Tsap enzyme. Bothfragments were ligated and clones with correct insertion and correctsequence of the left ITR were selected. To enable liberation of the leftITR from the vector sequences at the time of virus generation, a NotIsite flanking the left ITR was introduced by PCR. From this clone, theE1 sequences were deleted and replaced by a polylinker sequence usingPCR. The polylinker sequence is used to introduce an expression cassettefor a gene of choice.

Recombinant Ad35 clones are generated by transfection of PER.C6 cellswith the adapter plasmid, pBr/Ad35.pIX-EcoA and pBr/Ad35.Sal2-rITR asshown in FIG. 3. Homologous recombination gives rise to recombinantviruses.

Example 5 The Prevalence of Neutralizing Activity (NA) to Ad35 is Low inHuman Sera from Different Geographic Locations

In Example 1, the analysis of neutralizing activity (“NA”) in human serafrom one location in Belgium was described. Strikingly, of a panel of 44adenovirus serotypes tested, one serotype, Ad35, was not neutralized inany of the 100 sera assayed. In addition, a few serotypes, Ad26, Ad34and Ad48 were found to be neutralized in 8%, or less, of the seratested. This analysis was further extended to other serotypes ofadenovirus not previously tested and, using a selection of serotypesfrom the first screen, was also extended to sera from differentgeographic locations.

Hereto, adenoviruses were propagated, purified and tested forneutralization in the CPE-inhibition assay as described in Example 1.Using the sera from the same batch as in Example 1, adenovirus serotypes7B, 11, 14, 18 and 44/1876 were tested for neutralization. These viruseswere found to be neutralized in, respectively, 59, 13, 30, 98 and 54% ofthe sera. Thus, of this series, Ad11 is neutralized with a relativelylow frequency.

Since it is known that the frequency of isolation of adenovirusserotypes from human tissue as well as the prevalence of NA toadenovirus serotypes may differ on different geographic locations, wefurther tested a selection of the adenovirus serotypes against sera fromdifferent places. Human sera were obtained from two additional places inEurope (Bristol, UK and Leiden, NL) and from two places in the UnitedStates (Stanford, Calif. and Great Neck, N.Y.). Adenoviruses that werefound to be neutralized in 20% or less of the sera in the first screen,as well as Ad2, Ad5, Ad27, Ad30, Ad38, Ad43, were tested forneutralization in sera from the UK. The results of these experiments arepresented in FIG. 4.

Adenovirus serotypes 2 and 5 were again neutralized in a high percentageof human sera. Furthermore, some of the serotypes that were neutralizedin a low percentage of sera in the first screen are neutralized in ahigher percentage of sera from the UK, e.g., Ad26 (7% vs. 30%), Ad28(13% vs. 50%), Ad34 (5% vs. 27%) and Ad48 (8% vs. 32%). Neutralizingactivity against Ad11 and Ad49 that were found in a relatively lowpercentage of sera in the first screen, were found in an even lowerpercentage of sera in this second screen (13% vs. 5% and 20% vs. 11%,respectively). Serotype Ad35 that was not neutralized in any of the serain the first screen, was now found to be neutralized in a low percentage(8%) of sera from the UK. The prevalence of NA in human sera from the UKis the lowest to serotypes Ad11 and Ad35.

For further analysis, sera obtained from two locations in the US(Stanford, Calif. and Great Neck, N.Y.) and from The Netherlands(Leiden). FIG. 5 presents an overview of data obtained with these seraand the previous data. Not all viruses were tested in all sera, exceptfor Ad5, Ad11 and Ad35. The overall conclusion from this comprehensivescreen of human sera is that the prevalence of neutralizing activity toAd35 is the lowest of all serotypes throughout the western countries: onaverage 7% of the human sera contain neutralizing activity (fivedifferent locations). Another B-group adenovirus, Ad11 is alsoneutralized in a low percentage of human sera (average 11% in sera fromfive different locations). Adenovirus type 5 is neutralized in 56% ofthe human sera obtained from five different locations. Although nottested in all sera, D-group serotype 49 is also neutralized withrelatively low frequency in samples from Europe and from one location ofthe US (average 14%).

In the herein described neutralization experiments, a serum is judgednon-neutralizing when, in the well with the highest serum concentration,the maximum protection of CPE is 40% compared to the controls withoutserum. The protection is calculated as follows:

${\% \mspace{14mu} {protection}} = {\frac{{O\; D{\mspace{11mu} \;}{corresponding}\mspace{14mu} {well}} - {O\; D\mspace{14mu} {virus}\mspace{14mu} {control}}}{{O\; D\mspace{14mu} {non}\text{-}{infected}\mspace{14mu} {control}} - {O\; D\mspace{14mu} {virus}\mspace{14mu} {control}}} \times 100\%}$

As described in Example 1, the serum is plated in five differentdilutions ranging from 4× to 64× diluted. Therefore, it is possible todistinguish between low titers (i.e., neutralization only in the highestserum concentrations) and high titers of NA (i.e., also neutralizationin wells with the lowest serum concentration). Of the human sera used inour screen that were found to contain neutralizing activity to Ad5, 70%turned out to have high titers whereas of the sera that contained NA toAd35, only 15% had high titers. Of the sera that were positive for NA toAd11 only 8% had high titers. For Ad49, this was 5%. Therefore, not onlyis the frequency of NA to Ad35, Ad11 and Ad49 much lower as compared toAd5, but of the sera that do contain NA to these viruses, the vastmajority have low titers. Adenoviral vectors based on Ad11, Ad35 or Ad49have, therefore, a clear advantage over Ad5 based vectors when used asgene therapy vehicles or vaccination vectors in vivo or in anyapplication where infection efficiency is hampered by neutralizingactivity.

In the following examples, the construction of a vector system for thegeneration of safe, RCA-free Ad35-based vectors is described.

Example 6 Sequence of the Human Adenovirus type 35

Ad35 viruses were propagated on PER.C6 cells and DNA was isolated asdescribed in Example 4. The total sequence was generated by QiagenSequence Services (Qiagen GmbH, Germany). Total viral DNA was sheared bysonification and the ends of the DNA were made blunt by T4 DNApolymerase. Sheared blunt fragments were size fractionated on agarosegels and gel slices corresponding to DNA fragments of 1.8 to 2.2 kb wereobtained. DNA was purified from the gel slices by the QIAquick gelextraction protocol and subcloned into a shotgun library of pUC19plasmid cloning vectors. An array of clones in 96-well plates coveringthe target DNA 8 (+/−2) times was used to generate the total sequence.Sequencing was performed on Perkin-Elmer 9700 thermocyclers using BigDye Terminator chemistry and AmpliTaq FS DNA polymerase followed bypurification of sequencing reactions using QIAGEN DyeEx 96 technology.Sequencing reaction products were then subjected to automated separationand detection of fragments on ABI 377 XL 96 lane sequencers. Initialsequence results were used to generate a contig sequence and gaps werefilled in by primer walking reads on the target DNA or by directsequencing of PCR products. The ends of the virus turned out to beabsent in the shotgun library, most probably due to cloning difficultiesresulting from the amino acids of pTP that remain bound to the ITRsequences after proteinase K digestion of the viral DNA. Additionalsequence runs on viral DNA solved most of the sequence in those regions,however it was difficult to obtain a clear sequence of the most terminalnucleotides. At the 5 end the sequence portion obtained was5-CCAATAATATACCT-3 (SEQ ID NO:38) while at the 3 end, the obtainedsequence portion was 5-AGGTATATTATTGATGATGGG-3 (SEQ ID NO:39). Mosthuman adenoviruses have a terminal sequence 5-CATCATCAATAATATACC-3 (SEQID NO:40). In addition, a clone representing the 3 end of the Ad35 DNAobtained after cloning the terminal 7 kb Ad35 EcoRI fragment into pBr322(see, Example 4) also turned out to have the typical CATCATCAATAAT . . .sequence as seen in SEQ ID NO:40. Therefore, Ad35 may have the typicalend sequence and the differences obtained in sequencing directly on theviral DNA are due to artifacts correlated with run-off sequence runs andthe presence of residual amino acids of pTP.

The total sequence of Ad35 with corrected terminal sequences is given inFIG. 6. Based upon sequence homology with Ad5 (Genbank # M72360) and Ad7(partial sequence Genbank # X03000) and on the location of open readingframes, the organization of the virus is identical to the generalorganization of most human adenoviruses, especially the subgroup Bviruses. The total length of the genome is 34,794 basepairs.

Example 7 Construction of a Plasmid-Based Vector System to GenerateRecombinant Ad35-Based Viruses

A functional plasmid-based vector system to generate recombinantadenoviral vectors comprises the following components:

1. An adapter plasmid comprising a left ITR and packaging sequencesderived from Ad35 and at least one restriction site for insertion of aheterologous expression cassette and lacking E1 sequences. Furthermore,the adapter plasmid contains Ad35 sequences 3 from the E1B coding regionincluding the pIX promoter and coding sequences enough to mediatehomologous recombination of the adapter plasmid with a second nucleicacid molecule.

2. A second nucleic acid molecule, comprising sequences homologous tothe adapter plasmid, and Ad35 sequences necessary for the replicationand packaging of the recombinant virus, that is, early, intermediate andlate genes that are not present in the packaging cell.

3. A packaging cell providing at least functional E1 proteins capable ofcomplementing the E1 function of Ad35.

Other methods for the generation of recombinant adenoviruses oncomplementing packaging cells are known in the art, and may be appliedto Ad35 viruses without departing from the invention. As an example, theconstruction of a plasmid-based system, as outlined above, is describedin detail below.

1) Construction of Ad35 Adapter Plasmids

Hereto, the adapter plasmid pAdApt (FIG. 7; described in Example 2) wasfirst modified to obtain adapter plasmids that contain extendedpolylinkers and that have convenient unique restriction sites flankingthe left ITR and the adenovirus sequence at the 3 end to enableliberation of the adenovirus insert from plasmid vector sequences.Construction of these plasmids is described below in detail:

Adapter plasmid pAdApt (Example 2) was digested with SalI and treatedwith Shrimp Alkaline Phosphatase to reduce religation. A linker,composed of the following two phosphorylated and annealed oligos:ExSalPacF 5-TCG ATG GCA AAC AGC TAT TAT GGG TAT TAT GGG TTC GAA TTA ATTAA-3 (SEQ ID NO:41); and ExSalPacR 5-TCG ATT AAT TAA TTC GAA CCC ATA ATACCC ATA ATA GCT GTT TGC CA-3 (SEQ ID NO:42); was directly ligated intothe digested construct, thereby replacing the SalI restriction site byPi-PspI, SwaI and PacI. This construct was designated pADAPT+ExSalPaclinker. Furthermore, part of the left ITR of pAdApt was amplified by PCRusing the following primers: PCLIPMSF: 5-CCC CAA TTG GTC GAC CAT CAT CAATAA TAT ACC TTA TTT TGG-3 (SEQ ID NO:43) and pCLIPBSRGI: 5-GCG AAA ATTGTC ACT TCC TGT G-3 (SEQ ID NO:44). The amplified fragment was digestedwith MunI and BsrGI and cloned into pAd5/Clip (see, Example 2), whichwas partially digested with EcoRI and, after purification, digested withBsrGI, thereby re-inserting the left ITR and packaging signal. Afterrestriction enzyme analysis, the construct was digested with ScaI andSgrAI and an 800 bp fragment was isolated from gel and ligated intoScaI/SgrAI-digested pADAPT+ExSalPac linker. The resulting construct,designated pIPspSalAdapt, was digested with SalI, dephosphorylated, andligated to the phosphorylated ExSalPacF/ExSalPacR double-stranded linkerpreviously mentioned. A clone in which the PacI site was closest to theITR was identified by restriction analysis and sequences were confirmedby sequence analysis. This novel pAdApt construct, termed pIPspAdapt(FIG. 8) thus harbours two ExSalPac linkers containing recognitionsequences for PacI, PI-PspI and BstBI, which surround the adenoviralpart of the adenoviral adapter construct, and which can be used tolinearize the plasmid DNA prior to cotransfection with adenoviral helperfragments.

In order to further increase transgene cloning permutations, a number ofpolylinker variants were constructed based on pIPspAdapt. For thispurpose, pIPspAdapt was first digested with EcoRI and dephosphorylated.A linker composed of the following two phosphorylated and annealedoligos: Ecolinker+: 5-AAT TCG GCG CGC CGT CGA CGA TAT CGA TAG CGG CCGC-3 (SEQ ID NO:45) and Ecolinker−: 5-AAT TGC GGC CGC TAT CGA TAT CGT CGACGG CGC GCC G-3 (SEQ ID NO:46) was ligated into this construct, therebycreating restriction sites for AscI, SalI, EcoRV, ClaI and NotI. Bothorientations of this linker were obtained, and sequences were confirmedby restriction analysis and sequence analysis. The plasmid containingthe polylinker in the order 5 HindIII, KpnI, AgeI, EcoRI, AscI, SalI,EcoRV, ClaI, NotI, NheI, HpaI, BamHI and XbaI was termed pIPspAdapt1(FIG. 9), while the plasmid containing the polylinker in the orderHindIII, KpnI, AgeI, NotI, ClaI, EcoRV, SalI, AscI, EcoRI, NheI, HpaI,BamHI and XbaI was termed pIPspAdapt2.

To facilitate the cloning of other sense or antisense constructs, alinker composed of the following two oligonucleotides was designed, toreverse the polylinker of pIPspAdapt: HindXba+ 5-AGC TCT AGA GGA TCC GTTAAC GCT AGC GAA TTC ACC GGT ACC AAG CTT A-3 (SEQ ID NO:47); HindXba−5-CTA GTA AGC TTG GTA CCG GTG AAT TCG CTA GCG TTA ACG GAT CCT CTA G-3(SEQ ID NO:48). This linker was ligated into HindIII/XbaI-digestedpIPspAdapt and the correct construct was isolated. Confirmation was doneby restriction enzyme analysis and sequencing. This new construct,pIPspAdaptA, was digested with EcoRI and the previously mentionedEcolinker was ligated into this construct. Both orientations of thislinker were obtained, resulting in pIPspAdapt3 (FIG. 10), which containsthe polylinker in the order XbaI, BamHI, HpaI, NheI, EcoRI, AscI, SalI,EcoRV, ClaI, NotI, AgeI, KpnI and HindIII. All sequences were confirmedby restriction enzyme analysis and sequencing.

Adapter plasmids based on Ad35 were then constructed as follows:

The left ITR and packaging sequence corresponding to Ad35 wt sequencesnucleotides 1 to 464 (FIG. 6) were amplified by PCR on wtAd35 DNA usingthe following primers: Primer 35F1: 5-CGG AAT TCT TAA TTA ATC GAC ATCATC AAT AAT ATA CCT TAT AG-3 (SEQ ID NO:49) and Primer 35R2: 5-GGT GGTCCT AGG CTG ACA CCT ACG TAA AAA CAG-3 (SEQ ID NO:50). Amplificationintroduces a PacI site at the 5 end and an AvrII site at the 3 end ofthe sequence.

For the amplification, Platinum Pfx DNA polymerase enzyme (LTI) was usedaccording to manufacturer's instructions, but with primers at 0.6 M andwith DMSO added to a final concentration of 3%. Amplification programwas as follows: two minutes at 94° C., (30 seconds at 94° C., 30 secondsat 56° C., one minute at 68° C.) for 30 cycles, followed by ten minutesat 68° C.

The PCR product was purified using a PVR purification kit (LTI)according to the manufacturer's instructions, and digested with PacI andAvrII. The digested fragment was then purified from gel using theGENECLEAN kit (Bio 101, Inc.). The Ad5-based adapter plasmidpIPspAdApt-3 (FIG. 10) was digested with AvrII and then partially withPacI and the 5762 bp fragment was isolated in an LMP agarose gel sliceand ligated with the abovementioned PCR fragment digested with the sameenzymes and transformed into electrocompetent DH10B cells (LTI). Theresulting clone is designated pIPspAdApt3-Ad35lITR.

In parallel, a second piece of Ad35 DNA was amplified using thefollowing primers: 35F3: 5-TGG TGG AGA TCT GGT GAG TAT TGG GAA AAC-3(SEQ ID NO:51) and 35R4: 5-CGG AAT TCT TAA TTA AGG GAA ATG CAA ATC TGTGAG G-3 (SEQ ID NO:52).

The sequence of this fragment corresponds to nucleotides 3401 to 4669 ofwtAd35 (FIG. 6) and contains 1.3 kb of sequences starting directly 3from the E1B 55k coding sequence. Amplification and purification weredone as previously described herein for the fragment containing the leftITR and packaging sequence. The PCR fragment was then digested with PacIand subcloned into pNEB193 vector (New England Biolabs) digested withSmaI and PacI. The integrity of the sequence of the resulting clone waschecked by sequence analysis. pNEB/Ad35 pF3R4 was then digested withBglII and PacI and the Ad35 insert was isolated from gel using theQIAExII kit (Qiagen). pIPspAdApt3-Ad35lITR was digested with BglII andthen partially with PacI. The 3624 bp fragment (containing vectorsequences, the Ad35 ITR and packaging sequences as well as the CMVpromoter, multiple cloning region and polyA signal) was also isolatedusing the QIAExII kit (Qiagen). Both fragments were ligated andtransformed into competent DH10B cells (LTI). The resulting clone,pAdApt35IP3 (FIG. 11), has the expression cassette from pIPspAdApt3 butcontains the Ad35 left ITR and packaging sequences and a second fragmentcorresponding to nucleotides 3401 to 4669 from Ad35. A second version ofthe Ad35 adapter plasmid having the multiple cloning site in theopposite orientation was made as follows:

pIPspAdapt1 (FIG. 9) was digested with NdeI and BglII and the 0.7 kbpband containing part of the CMV promoter, the MCS and SV40 polyA wasisolated and inserted in the corresponding sites of pAdApt35IP3generating pAdApt35IP1 (FIG. 12).

pAdApt35.LacZ and pAdApt35.Luc adapter plasmids were then generated byinserting the transgenes from pcDNA.LacZ (digested with KpnI and BamHI)and pAdApt.Luc (digested with HindIII and BamHI) into the correspondingsites in pAdApt35IP1. The generation of pcDNA.LacZ and pAdApt.Luc isdescribed in International Patent Application WO99/55132.

Construction of Cosmid pWE.Ad35.pXI-rITR

FIG. 13 presents the various steps undertaken to construct the cosmidclone containing Ad35 sequences from bp 3401 to 34794 (end of the rightITR) that are described in detail below.

A first PCR fragment (pIX-NdeI) was generated using the following primerset:

35F5: (SEQ ID NO:53) 5-CGG AAT TCG CGG CCG CGG TGA GTA TTG GGA AAA C-3and 35R6: (SEQ ID NO:54) 5-CGC CAG ATC GTC TAC AGA ACA G-3.

DNA polymerase Pwo (Roche) was used according to manufacturer'sinstructions, however, with an end concentration of 0.6 M of bothprimers and using 50 ngr wt Ad35 DNA as template. Amplification was doneas follows: two minutes at 94° C., 30 cycles of 30 seconds at 94° C., 30seconds at 65° C. and one minute 45 seconds at 72° C., followed by eightminutes at 68° C. To enable cloning in the TA cloning vector PCR2.1, alast incubation with 1 unit superTaq polymerase (HT Biotechnology LTD)for ten minutes at 72° C. was performed.

The 3370 bp amplified fragment contains Ad35 sequences from bp 3401 to6772 with a NotI site added to the 5 end. Fragments were purified usingthe PCR purification kit (LTI).

A second PCR fragment (NdeI-rITR) was generated using the followingprimers:

35F7: (SEQ ID NO:55) 5-GAA TGC TGG CTT CAG TTG TAA TC-3 and 35R8: (SEQID NO:56) 5-CGG AAT TCG CGG CCG CAT TTA AAT CAT CAT CAA TAA TAT ACC-3.

Amplification was done with pfx DNA polymerase (LTI) according tomanufacturer's instructions but with 0.6 M of both primers and 3% DMSOusing 10 ngr. of wtAd35 DNA as template. The program was as follows:three minutes at 94° C. and five cycles of 30 seconds at 94° C., 45seconds at 40° C., two minutes 45 seconds at 68° C., followed by 25cycles of 30 seconds at 94° C., 30 seconds at 60° C., two minutes 45seconds at 68° C. To enable cloning in the TA-cloning vector PCR2.1, alast incubation with 1 unit superTaq polymerase for ten minutes at 72°C. was performed. The 1.6 kb amplified fragment ranging from nucleotides33178 to the end of the right ITR of Ad35, was purified using the PCRpurification kit (LTI).

Both purified PCR fragments were ligated into the PCR2.1 vector of theTA-cloning kit (Invitrogen) and transformed into STBL-2 competent cells(LTI). Clones containing the expected insert were sequenced to confirmcorrect amplification. Next, both fragments were excised from the vectorby digestion with NotI and NdeI and purified from gel using theGENECLEAN kit (BIO 101, Inc.). Cosmid vector pWE15 (Clontech) wasdigested with NotI, dephosphorylated and also purified from gel. Thesethree fragments were ligated and transformed into STBL2 competent cells(LTI). One of the correct clones that contained both PCR fragments wasthen digested with NdeI, and the linear fragment was purified from gelusing the GENECLEAN kit. Ad35 wt DNA was digested with NdeI and the 26.6kb fragment was purified from LMP gel using agarase enzyme (Roche)according to the manufacturer's instructions. These fragments wereligated together and packaged using phage packaging extracts(Stratagene) according to the manufacturer's protocol. After infectioninto STBL-2 cells, colonies were grown on plates and analyzed forpresence of the complete insert. One clone with the large fragmentinserted in the correct orientation and having the correct restrictionpatterns after independent digestions with three enzymes (NcoI, PvuIIand ScaI) was selected. This clone is designated pWE.Ad35.pIX-rITR. Itcontains the Ad35 sequences from bp 3401 to the end and is flanked byNotI sites (FIG. 14).

Generation of Ad35 Based Recombinant Viruses on PER.C6

Wild-type Ad35 virus can be grown on PER.C6 packaging cells to very hightiters. However, whether the Ad5-E1 region that is present in PER.C6 isable to complement E1-deleted Ad35 recombinant viruses is unknown. Totest this, PER.C6 cells were cotransfected with the above describedadapter plasmid pAdApt35.LacZ and the large backbone fragmentpWE.Ad35.pIX-rITR. First, pAdApt35.LacZ was digested with PacI andpWE.Ad35.pIX-rITR was digested with NotI. Without further purification,4 gr of each construct was mixed with DMEM (LTI) and transfected intoPER.C6 cells, seeded at a density of 5×10⁶ cells in a T25 flask the daybefore, using Lipofectamin (LTI) according to the manufacturer'sinstructions. As a positive control, 6 gr of PacI-digestedpWE.Ad35.pIX-rITR DNA was cotransfected with a 6.7 kb NheI fragmentisolated from Ad35 wt DNA containing the left end of the viral genomeincluding the E1 region. The next day, medium (DMEM with 10% FBS and 10mM MgCl₂) was refreshed and cells were further incubated. At day 2following the transfection, cells were trypsinized and transferred toT80 flasks. The positive control flask showed CPE at five days followingtransfection, showing that the pWE.Ad35.pIX-rITR construct is functionalat least in the presence of Ad35-E1 proteins. The transfection with theAd35 LacZ adapter plasmid and pWE.Ad35.pIX-rITR did not give rise toCPE. These cells were harvested in the medium at day 10 andfreeze/thawed once to release virus from the cells. 4 ml of theharvested material was added to a T80 flask with PER.C6 cells (at 80%confluency) and incubated for another five days. Thisharvest/re-infection was repeated for two times but there was noevidence for virus-associated CPE.

From this experiment, it seems that the Ad5-E1 proteins are not, or notwell enough, capable of complementing Ad35 recombinant viruses, however,it may be that the sequence overlap of the adapter plasmid and thepWE.Ad35.pIX-rITR backbone plasmid is not large enough to efficientlyrecombine and give rise to a recombinant virus genome. The positivecontrol transfection was done with a 6.7 kb left end fragment andtherefore the sequence overlap was about 3.5 kb. The adapter plasmid andthe pWE.Ad35.pIX-rITR fragment have a sequence overlap of 1.3 kb. Tocheck whether the sequence overlap of 1.3 kb is too small for efficienthomologous recombination, a cotransfection was done with PacI-digestedpWE.Ad35.pIX-rITR and a PCR fragment of Ad35 wt DNA generated with theabove mentioned 35F1 and 35R4 using the same procedures as previouslydescribed herein. The PCR fragment thus contains left end sequences upto bp 4669 and, therefore, has the same overlap sequences withpWE.Ad35.pIX-rITR as the adapter plasmid pAdApt35.LacZ, but has Ad35 E1sequences. Following PCR column purification, the DNA was digested withSalI to remove possible intact template sequences. A transfection withthe digested PCR product alone served as a negative control. Four daysafter the transfection, CPE occurred in the cells transfected with thePCR product and the Ad35 pIX-rITR fragment, and not in the negativecontrol. This result shows that a 1.3 kb overlapping sequence issufficient to generate viruses in the presence of Ad35 E1 proteins. Fromthese experiments, we conclude that the presence of at least one of theAd35.E1 proteins is necessary to generate recombinant Ad35-based vectorsfrom plasmid DNA on Ad5-complementing cell lines.

Example 8 Construction of Ad35.E1 Expression Plasmids

Since Ad5-E1 proteins in PER.C6 are incapable of complementing Ad35recombinant viruses efficiently, Ad35 E1 proteins have to be expressedin Ad5-complementing cells (e.g., PER.C6). Otherwise, a new packagingcell line expressing Ad35 E1 proteins has to be made, starting fromeither diploid primary human cells or established cell lines notexpressing adenovirus E1 proteins. To address the first possibility, theAd35 E1 region was cloned in expression plasmids as described below.

First, the Ad35 E1 region from bp 468 to bp 3400 was amplified fromwtAd35

DNA using the following primer set: 35F11: 5-GGG GTA CCG AAT TCT CGC TAGGGT ATT TAT ACC-3 (SEQ ID NO:57) and 35F10: 5-GCT CTA GAC CTG CAG GTTAGT CAG TTT CTT CTC CAC TG-3 (SEQ ID NO:58). This PCR introduces a KpnIand EcoRI site at the 5 end and an SbfI and XbaI site at the 3 end.

Amplification on 5 ngr. template DNA was done with Pwo DNA polymerase(Roche) using the manufacturer's instructions, however, with bothprimers at a final concentration of 0.6 M. The program was as follows:two minutes at 94° C., five cycles of 30 seconds at 94° C., 30 secondsat 56° C. and two minutes at 72° C., followed by 25 cycles of 30 secondsat 94° C., 30 seconds at 60° C. and two minutes at 72° C., followed byten minutes at 72° C. PCR product was purified by a PCR purification kit(LTI) and digested with KpnI and XbaI. The digested PCR fragment wasthen ligated to the expression vector pRSVhbvNeo (see below) alsodigested with KpnI and XbaI. Ligations were transformed into competentSTBL-2 cells (LTI) according to manufacturer's instructions and colonieswere analyZed for the correct insertion of Ad35E1 sequences into thepolylinker in between the RSV promoter and HBV polyA. The resultingclone was designated pRSV.Ad35-E1 (FIG. 15). The Ad35 sequences inpRSV.Ad35-E1 were checked by sequence analysis.

pRSVhbvNeo was generated as follows: pRc-RSV (Invitrogen) was digestedwith PvuII, dephosphorylated with TSAP enzyme (LTI), and the 3 kb vectorfragment was isolated in low melting point agarose (LMP). PlasmidpPGKneopA (FIG. 16; described in International Patent ApplicationWO96/35798) was digested with SspI completely to linearize the plasmidand facilitate partial digestion with PvuII. Following the partialdigestion with PvuII, the resulting fragments were separated on a LMPagarose gel and the 2245 bp PvuII fragment, containing the PGK promoter,neomycin-resistance gene and HBVpolyA, was isolated. Both isolatedfragments were ligated to give the expression vector pRSV-pNeo that nowhas the original SV40prom-neo-SV40polyA expression cassette replaced bya PGKprom-neo-HBVpolyA cassette (FIG. 17). This plasmid was furthermodified to replace the BGHpA with the HBVpA as follows: pRSVpNeo waslinearized with ScaI and further digested with XbaI. The 1145 bpfragment, containing part of the Amp gene and the RSV promoter sequencesand polylinker sequence, was isolated from gel using the GeneClean kit(Bio Inc. 101). Next, pRSVpNeo was linearized with ScaI and furtherdigested with EcoRI partially and the 3704 bp fragment containing thePGKneo cassette and the vector sequences were isolated from gel asabove. A third fragment, containing the HBV polyA sequence flanked byXbaI and EcoRI at the 5 and 3 end respectively, was then generated byPCR amplification on pRSVpNeo using the following primer set: HBV-F:5-GGC TCT AGA GAT CCT TCG CGG GAC GTC-3 (SEQ ID NO:59) and HBV-R: 5-GGCGAA TTC ACT GCC TTC CAC CAA GC-3 (SEQ ID NO:60).

Amplification was done with Elongase enzyme (LTI) according to themanufacturer's instructions with the following conditions: 30 seconds at94° C., then five cycles of 45 seconds at 94° C., one minute at 42° C.and one minute 68° C., followed by 30 cycles of 45 seconds at 94° C.,one minute at 65° C. and one minute at 68° C., followed by ten minutesat 68° C. The 625 bp PCR fragment was then purified using the QiaquickPCR purification kit, digested with EcoRI and XbaI and purified from gelusing the GENECLEAN kit. The three isolated fragments were ligated andtransformed into DH5 competent cells (LTI) to give the constructpRSVhbvNeo (FIG. 18). In this construct, the transcription regulatoryregions of the RSV expression cassette and the neomycin selection markerare modified to reduce overlap with adenoviral vectors that oftencontain CMV and SV40 transcription regulatory sequences.

Generation of Ad35 Recombinant Viruses on PER.C6 Cells Cotransfectedwith an Ad35-E1 Expression Construct

PER.C6 cells were seeded at a density of 5×10⁶ cells in a T25 flask and,the next day, transfected with a DNA mixture containing:

1 g pAdApt35.LacZ digested with PacI

5 g pRSV.Ad35E1 undigested

2 g pWE.Ad35.pIX-rITR digested with NotI

Transfection was done using Lipofectamine according to themanufacturer's instructions. Five hours after addition of thetransfection mixture to the cells, medium was removed and replaced byfresh medium. After two days, cells were transferred to T80 flasks andfurther cultured. One week post-transfection, 1 ml of the medium wasadded to A549 cells and, the following day, cells were stained for LacZexpression. Blue cells were clearly visible after two hours of stainingindicating that recombinant LacZ expressing viruses were produced. Thecells were further cultured, but no clear appearance of CPE was noted.However, after 12 days, clumps of cells appeared in the monolayer and 18days following transfection, cells were detached. Cells and medium werethen harvested, freeze-thawed once, and 1 ml of the crude lysate wasused to infect PER.C6 cells in a 6-well plate. Two days after infection,cells were stained for LacZ activity. After two hours, 15% of the cellswere stained blue. To test for the presence of wt and/or replicatingcompetent viruses, A549 cells were infected with these viruses andfurther cultured. No signs of CPE were found indicating the absence ofreplication competent viruses. These experiments show that recombinantAdApt35.LacZ viruses were made on PER.C6 cells cotransfected with anAd35-E1 expression construct.

Ad35 recombinant viruses escape neutralization in human serum containingneutralizing activity to Ad5 viruses.

The AdApt35.LacZ viruses were then used to investigate infection in thepresence of serum that contains neutralizing activity to Ad5 viruses.Purified Ad5-based LacZ virus served as a positive control for NA.Hereto, PER.C6 cells were seeded in a 24-well plate at a density of2×10⁵ cells/well. The next day, a human serum sample with highneutralizing activity to Ad5 was diluted in culture medium in five stepsof five times dilutions. 0.5 ml of diluted serum was then mixed with4×10⁶ virus particles AdApt5.LacZ virus in 0.5 ml medium and, after 30minutes of incubation at 37° C., 0.5 ml of the mixture was added toPER.C6 cells in duplicate. For the AdApt35.LacZ viruses, 0.5 ml of thediluted serum samples were mixed with 0.5 ml crude lysate containingAdApt35.LacZ virus and, after incubation, 0.5 ml of this mixture wasadded to PER.C6 cells in duplo. Virus samples incubated in mediumwithout serum were used as positive controls for infection. After twohours of infection at 37° C., medium was added to reach a final volumeof 1 ml and cells were further incubated. Two days after infection,cells were stained for LacZ activity. The results are shown in Table II.From these results, it is clear that whereas AdApt5.LacZ viruses areefficiently neutralized, AdApt35.LacZ viruses remain infectiousirrespective of the presence of human serum. This proves thatrecombinant Ad35-based viruses escape neutralization in human sera thatcontain NA to Ad5-based viruses.

Example 9 An Ad5/Fiber35 Chimeric Vector with Cell Type Specificity forHemopoietic CD34⁺Lin⁻ Stem Cells

In Example 3, we described the generation of a library of Ad5 basedadenoviruses harboring fiber proteins of other serotypes. As anon-limiting example for the use of this library, we here describe theidentification of fiber-modified adenoviruses that show improvedinfection of hemopoietic stem cells.

Cells isolated from human bone marrow, umbilical cord blood, ormobilized peripheral blood carrying the flow cytometric phenotype ofbeing positive for the CD34 antigen and negative for the earlydifferentiation markers CD33, CD38, and CD71 (lin⁻) are commonlyreferred to as hemopoietic stem cells (HSC). Genetic modification ofthese cells is of major interest since all hemopoietic lineages arederived from these cells and therefore the HSC is a target cell for thetreatment of many acquired or congenital human hemopoietic disorders.Examples of diseases that are possibly amenable for genetic modificationof HSC include, but are not limited to, Hurlers disease, Hunter'sdisease, Sanfilippos disease, Morquios disease, Gaucher disease, Farbersdisease, Niemann-Pick disease, Krabbe disease, MetachromaticLeucodistrophy, 1-cell disease, severe immunodeficiency syndrome, Jak-3deficiency, Fucosidose deficiency, thallasemia, and erythropoieticporphyria. Besides these hemopoietic disorders, also strategies toprevent or treat acquired immunodeficiency syndrome (“AIDS”) andhemopoietic cancers are based on the genetic modification of HSCs (orcells derived from HSCs such as CD4 positive T lymphocytes in case ofAIDS). The examples listed herein thus aim at introducing DNA into theHSC in order to complement on a genetic level for a gene and proteindeficiency. In case of strategies for AIDS or cancer, the DNA to beintroduced into the HSC can be anti-viral genes or suicide genes.

Besides the examples listed herein, several other areas exist in whichefficient transduction of HSCs using adenoviral vectors can play animportant role, for instance, in the field of tissue engineering. Inthis area, it is important to drive differentiation of HSCs to specificlineages. Some, non-limiting, examples are ex vivo bone formation,cartilage formation, skin formation, as well as the generation of T-cellprecursors or endothelial cell precursors. The generation of bone,cartilage or skin in bioreactors can be used for transplantation afterbone fractures or spinal cord lesions or severe burn injuries.Naturally, transduced cells can also directly be re-infused into apatient. The formation of large numbers of endothelial cell precursorfrom HSCs is of interest since these endothelial precursor cells canhome, after re-infusion, to sites of cardiovascular injury such asischemia. Likewise, the formation of large numbers of T-cells from HSCsis of interest since these T-cell precursors can be primed, ex vivo, toeradicate certain targets in the human body after re-infusion of theprimed T-cells. Preferred targets in the human body can be tumors orvirus-infected cells.

From the herein described examples, it can be concluded that efficientgene delivery to HSCs is a major interest for the field of gene therapy.Therefore, alteration of the Ad5 host cell range to be able to targetHSCs in vitro as well as in vivo is a major interest hereof. To identifya chimeric adenovirus with preferred infection characteristics for humanHSCs, we generated a library of Ad5 based viruses carrying the fibermolecule from alternative adenoviral serotypes (serotypes 8, 9, 13, 16,17, 32, 35, 45, 40-L, 51). The generation of this fiber-modified libraryis described in Example 3 hereof. Ad5 was included as a reference. Asmall panel of this library was tested on human TF-1 (erythroidleukemia, ATCC CRL-2003) whereas all chimeric viruses generated weretested on human primary stroma cells and human HSCs. Human TF-1 cellswere routinely maintained in DMEM supplemented with 10% FCS and 50 ng/mlIL-3 (Sandoz, Basel, Switzerland). Human primary fibroblast-like stroma,isolated from a bone marrow aspirate, is routinely maintained inDMEM/10% FCS. Stroma was seeded at a concentration of 1×10⁵ cells perwell of 24-well plates. 24 hours after seeding cells were exposed fortwo hours to 1000 virus particles per cell of Ad5, Ad5.Fib16, Ad5.Fib17,Ad5.Fib35, Ad5.Fib40-L, or Ad5.Fib51 all carrying GFP as a marker. Aftertwo hours, cells were washed with PBS and reseeded in medium withoutaddition of virus. TF-1 cells were seeded at a concentration of 2×10⁵cells per well of 24-well plates and were also exposed for two hours to1000 virus particles of the different chimeric adenoviruses. Virus wasremoved by washing the cells after the two hours exposure. Both celltypes were harvested 48 hours after virus exposure and analyzed for GFPexpression using a flow cytometer. The results on TF-1 cells, shown inFIG. 19, demonstrate that chimeric adenoviruses carrying a fiber fromserotypes 16, 35, or 51 (all derived from adenovirus subgroup B) havepreferred infection characteristics as compared to Ad5 (subgroup C),Ad5.Fib17 (subgroup D), or Ad5.Fib40-L (subgroup F). Primary humanstroma was tested since these cells are commonly used as “feeder” cellsto allow proliferation and maintenance of HSCs under ex vivo cultureconditions. In contrast to the transduction of TF-1 cells, none of thefiber chimeric adenoviruses were able to efficiently transduce humanprimary stroma (FIG. 20). Reasonable infection of human fibroblast-likeprimary stroma was observed only with Ad5 despite the observation thatnone of the known receptor molecules are expressed on these cells (see,Table III). The absence of infection of human stroma using the chimericviruses is advantageous since, in a co-culture setting, the chimericadenovirus will not be absorbed primarily by the stroma “feeder” cells.

To test the transduction capacity of the fiber chimeric viruses, a poolof umbilical cord blood (three individuals) was used for the isolationof stem cells. CD34⁺ cells were isolated from mononuclear cellpreparation using a MACS laboratory separation system (Miltenyi Biotec)using the protocol supplied by the manufacturer. Of the CD34⁺ cells,2×10⁵ were seeded in a volume of 150 l DMEM (no serum; Gibco,Gaithersburg, Md.) and 10 l of chimeric adenovirus (to give a finalvirus particles/cell ratio of 1000) was added. The chimeric adenovirusestested were Ad5, Ad5.Fib16, Ad5.Fib35, Ad5Fib17, Ad5.Fib51 allcontaining GFP as a marker. Cells were incubated for two hours in ahumidified atmosphere of 10% CO₂ at 37° D. Thereafter, cells were washedonce with 500 l DMEM and re-suspended in 500 l of StemPro-34 SF medium(Life Technologies, Grand Island, N.Y.).

Cells were then cultured for five days in 24-well plates (Greiner,Frickenhausen, Germany) on irradiated (20 Gy) pre-established human bonemarrow stroma (ref 1), in a humidified atmosphere of 10% CO² at 37° C.After five days, the entire cell population was collected bytrypsinization with 100 l 0.25% Trypsin-EDTA (Gibco). The number ofcells before and after five days of culture was determined using ahematocytometer. The number of CD34⁺ and CD34⁺⁺CD33,38,71⁻ cells in eachsample was calculated from the total number of cells recovered and thefrequency of the CD34⁺⁺CD33,38,71⁻ cells in the whole population asdetermined by FACS analysis. The transduction efficiency was determinedby FACS analysis while monitoring, in distinct sub-populations, thefrequency of GFP expressing cells as well as the intensity of GFP perindividual cell. The results of this experiment, shown in FIG. 21,demonstrate that Ad5 or the chimeric adenovirus Ad5.Fib17 does notinfect CD34⁺Lin⁻ cells as witnessed by the absence of GFP expression. Incontrast, with the chimeric viruses carrying the fiber molecule ofserotypes 16, 51, or 35 high percentages of GFP positive cells arescored in this cell population. Specificity for CD34⁺Lin⁻ isdemonstrated since little GFP expression is observed in CD34⁺ cells thatare also expressing CD33, CD38, and CD71. Sub-fractioning of theCD34⁺Lin⁻ cells (FIG. 22) showed that the percentage of cells positivefor GFP declines using Ad5.Fib16, Ad5.Fib35, or Ad5.Fib51 when the cellsbecome more and more positive for the early differentiation markers CD33(myeloid), CD71 (erythroid), and CD38 (common early differentiationmarker). These results thus demonstrate the specificity of the chimericadenoviruses Ad5.Fib16, Ad5.Fib35, and Ad5.Fib51 for HSCs.

FIG. 23 shows an alignment of the Ad5 fiber with the chimeric B-groupfiber proteins derived from Ad16, 35 and 51. By determining the numberof cells recovered after the transduction procedure, the toxicity ofadenovirus can be determined. The recovery of the amount of CD34+ cellsas well as the amount of CD34⁺Lin⁻ (FIG. 24) demonstrates that a twohour exposure to 1000 adenovirus particles did not have an effect on thenumber of cells recovered.

Example 10 An Ad5/Fiber35 Chimeric Vector with Cell Type Specificity forDendritic Cells

Dendritic cells are antigen presenting cells (“APC”), specialized toinitiate a primary immune response, and able to boost a memory type ofimmune response. Dependent on their stage of development, DC displaydifferent functions: immature DC are very efficient in the uptake andprocessing of antigens for presentation by Major HistocompatibilityComplex (“MHC”) class I and class II molecules, whereas mature DC, beingless effective in antigen capture and processing, perform much better atstimulating naive and memory CD4⁺ and CD8⁺ T cells, due to the highexpression of MHC molecules and co-stimulatory molecules at their cellsurface. The immature DCs mature in vivo after uptake of antigen, travelto the T-cell areas in the lymphoid organs, and prime T-cell activation.

Since DCs are the cells responsible for triggering an immune response,there has been a long standing interest in loading DCs withimmunostimulatory proteins, peptides, or the genes encoding theseproteins, to trigger the immune system. The applications for thisstrategy are in the field of cancer treatment as well as in the field ofvaccination. So far, anti-cancer strategies have focussed primarily onex vivo loading of DCs with antigen (protein or peptide). These studieshave revealed that this procedure resulted in induction of cytotoxic Tcell activity. The antigens used to load the cells are generallyidentified as being tumor specific. Some, non-limiting, examples of suchantigens are GP100, mage, or Mart-1 for melanoma.

Besides treatment of cancer, many other potential human diseases arecurrently being prevented through vaccination. In the vaccinationstrategy, a “crippled” pathogen is presented to the immune system viathe action of the antigen presenting cells, i.e., the immature DCs.Well-known examples of disease prevention via vaccination strategiesinclude Hepatitis A, B, and C, influenza, rabies, yellow fever, andmeasles. Besides these well-known vaccination programs, researchprograms for treatment of malaria, ebola, river blindness, HIV and manyother diseases are being developed. Many of the identified pathogens areconsidered too dangerous for the generation of “crippled” pathogenvaccines. This latter thus calls for the isolation and characterizationof proteins of each pathogen to which a “full blown” immune response ismounted, thus resulting in complete protection upon challenge withwild-type pathogen.

For the strategy of loading DCs with immunostimulatory proteins orpeptides to become therapeutically feasible, at least two distinctcriteria have to be met. First, the isolation of large numbers of DCsthat can be isolated, manipulated, and re-infused into a patient, makingthe procedure autologous. To date, it is possible to obtain such largequantities of immature DCs from cultured peripheral blood monocytes fromany given donor. Second, a vector that can transduce DCs efficientlysuch that the DNA encoding for an immunostimulatory protein can bedelivered. The latter is extremely important since it has become clearthat the time required for DCs to travel to the lymphoid organs is suchthat most proteins or peptides are already released from the DCs,resulting in incomplete immune priming. Because DCs are terminallydifferentiated and thus non-dividing cells, recombinant adenoviralvectors are being considered for delivering the DNA encoding forantigens to DCs. Ideally, this adenovirus should have a high affinityfor dendritic cells, but should also not be recognized by neutralizingantibodies of the host such that in vivo transduction of DCs can beaccomplished. The latter would obviate the need for ex vivomanipulations of DCs but would result in a medical procedure identicalto the vaccination programs that are currently in place, i.e.,intramuscular or subcutaneous injection predominantly. Thus, DCtransduced by adenoviral vectors encoding an immunogenic protein may beideally suited to serve as natural adjuvants for immunotherapy andvaccination.

From the described examples, it can be concluded that efficient genedelivery to DCs is a major interest in the field of gene therapy.Therefore, alteration of the Ad5 host cell range to be able to targetDCs in vitro as well as in vivo is a major interest hereof. To identifya chimeric adenovirus with preferred infection characteristics for humanDCs, we generated a library of Ad5-based viruses carrying the fibermolecule from alternative serotypes (serotypes 8, 9, 13, 16, 17, 32, 35,45, 40-L, 51). Ad5 was included as a reference.

We evaluated the susceptibility of human monocyte derived immature andmature DC to recombinant chimeric adenoviruses expressing differentfibers.

Human PBMC from healthy donors were isolated through Ficoll-Hypaquedensity centrifugation. Monocytes were isolated from PBMC by enrichmentfor CD14⁺ cells using staining with FITC labelled anti-human CD 14monoclonal antibody (Becton Dickinson), anti-FITC microbeads and MACSseparation columns (Miltenyi Biotec).

This procedure usually results in a population of cells that are <90%CD14⁺ as analyzed by FACS. Cells were placed in culture using RPMI-1640medium (Gibco) containing 10% Foetal Bovine Serum (“FBS”) (Gibco), 200ng/ml rhu GM-CSF (R&D/ITK diagnostics, 100 ng/ml rhu IL-4 (R&D/ITKdiagnostics) and cultured for seven days with feeding of the cultureswith fresh medium containing cytokines on alternate days. After sevendays, the immature DC resulting from this procedure express a phenotypeCD83⁻,CD141^(low) or CD14⁻,HLA-DR⁺, as was demonstrated by FACSanalysis. Immature DCs are matured by culturing the cells in a mediumcontaining 100 ng/ml TNF-a for three days, after which, they expressedCD83 on their cell surface.

In a pilot experiment, 5×10⁵ immature DCs were seeded in wells of24-well plates and exposed for 24 hours to 100 and 1000 virus particlesper cell of each fiber recombinant virus. Virus tested was Ad5, and thefiber chimeric viruses based on Ad5: Ad5.Fib12, Ad5.Fib16, Ad5.Fib28,Ad5.Fib32, Ad5.Fib40-L (long fiber of serotype 40), Ad5.Fib49, andAd5.Fib51 (where Fibxx stands for the serotype from which the fibermolecule is derived). These viruses are derived from subgroup C, A, B,D, D, F, D, and B respectively. After 24 hours, cells were lysed (1%Triton X-100/PBS) and luciferase activity was determined using aprotocol supplied by the manufacturer (Promega, Madison, Wis., USA). Theresults of this experiment, shown in FIG. 25, demonstrate that Ad5poorly infects immature DCs as witnessed by the low level of transgeneexpression. In contrast, Ad5.Fib 16 and Ad5.Fib51 (both a B-group fiberchimeric virus) and also Ad5.Fib40-L (Subgroup F) show efficientinfection of immature DCs based on luciferase transgene expression.

In a second experiment, 5×10⁵ immature and mature DC were infected with10,000 virus particles per cell of Ad5, Ad5.Fib16, Ad5.Fib40-L, andAd5.Fib51 all carrying the LacZ gene as a marker. LacZ expression wasmonitored by flow cytometric analysis using a CM-FDG kit system and theinstructions supplied by the manufacturer (Molecular Probes, Leiden,NL). The results of this experiment, shown in FIG. 26, correlate withthe previous experiment in that Ad5.Fib16 and Ad5.Fib51 are superior toAd5 in transducing mature and immature human DCs. Also, this experimentshows that Ad5.Fib40-L is not as good as Ad5.Fib16 and Ad5.Fib51, but isbetter than Ad5.

Based on these results, we tested other chimeric adenoviruses containingfibers of B group viruses, for example, Ad5.Fib 11 and Ad5.Fib35 fortheir capacity to infect DCs. We focussed on immature DCs, since theseare the cells that process an expressed transgene product into MHC classI and II presentable peptides. Immature DCs were seeded at a celldensity of 5×10⁵ cells/well in 24-well plates (Costar) and infected with1,000 and 5,000 virus particles per cell, after which the cells werecultured for 48 hours under conditions for immature DCs prior to celllysis and Luciferase activity measurements. The results of thisexperiment, shown in FIG. 27, demonstrate that Ad5 based chimericadenoviruses containing fibers of group-B viruses efficiently infectimmature DCs. In a fourth experiment, we again infected immature DCsidentically as described in the former experiments but this time Ad5,Ad5.Fib16, and Ad5.Fib35 were used carrying GFP as a marker gene. Theresults on GFP expression measured with a flow cytometer 48 hours aftervirus exposure is shown in FIG. 28, and correlates with the dataobtained so far. Thus, the results so far are consistent in thatAd5-based vectors carrying a fiber from an alternative adenovirusderived from subgroup B, predominantly fiber of 35, 51, 16, and 11, aresuperior to Ad5 for transducing human DCs.

The adenoviruses disclosed herein are also very suitable for vaccinatinganimals. To illustrate this, we tested DCs derived from mice andchimpanzees to identify whether these viruses could be used in theseanimal models. The latter, in particular, since the receptor for humanadenovirus derived from subgroup B is unknown to date and therefore itis unknown whether this protein is conserved among species. For bothspecies, immature DCs were seeded at a density of 10⁵ cells per well of24-well plates. Cells were subsequently exposed for 48 hours to 1000virus particles per cell of Ad5, Ad5Fib 16, and Ad5.Fib51 in case ofmouse DC and Ad5, and Ad.Fib35 in case of chimpanzee DCs (see, FIG. 29).The mouse experiment was performed with viruses carrying luciferase as amarker, and demonstrated approximately 10 to 50-fold increasedluciferase activity as compared to Ad5.

The chimpanzee DCs were infected with the GFP viruses, and were analyzedusing a flow cytometer. These results (also shown in FIG. 29)demonstrate that Ad5 (3%) transduces chimpanzee DCs very poorly ascompared to Ad5.Fib35 (66.5%).

Example 11 Construction of a Plasmid-Based Vector System to GenerateAd11-Based Recombinant Viruses

The results of the neutralization experiments described in Example 5show that Ad11, like Ad35, was also not neutralized in the vast majorityof human serum samples. Therefore, recombinant adenoviruses based onAd11 are preferred above the commonly used Ad2 and Ad5-based vectors asvectors for gene therapy treatment and vaccination. Both Ad35 and Ad11are B-group viruses and are classified as viruses belonging to DNAhomology cluster 2 (Wadell, 1984). Therefore, the genomes of Ad35 andAd11 are very similar.

To generate a plasmid-based system for the production of Ad11-basedrecombinant viruses; the adapter plasmid pAdApt35IP1 generated inExample 7 is modified as follows. Construct pAdApt35IP1 is digested withAvrII and then partially with PacI. The digestion mixture is separatedon gel, and the 4.4 kb fragment containing the expression cassette andthe vector backbone is isolated using the GENECLEAN kit (BIO 101, Inc.).Then a PCR amplification is performed on wtAd11 DNA using the primers35F1 and 35R2 (see, Example 7) using Pwo DNA polymerase according to themanufacturer's instructions. The obtained PCR fragment of 0.5 kb ispurified using the PCR purification kit (LTI), and ligated to thepreviously prepared fragment of pAdApt35IP1. This gives constructpAdApt11-35IP1, in which the 5′ adenovirus fragment is exchanged for thecorresponding sequence of Ad11. Next, pAdApt11-35IP1 is digested withBglII and partially with PacI. The obtained fragments are separated ongel, and the 3.6 kb fragment containing the vector sequences, the 5′adenovirus fragment, and the expression cassette is purified from gel aspreviously described. Next, a PCR fragment is generated using primers35F3 and 35R4 (see, Example 7) on wtAd11 DNA. Amplification is done asabove and the obtained 1.3 kb fragment is purified and digested withBglII and PacI. The isolated fragments are then ligated to giveconstruct pAdApt11IP1. This adapter plasmid now contains Ad11 sequencesinstead of Ad35 sequences. Correct amplification of PCR amplified Ad11sequences is verified by comparison of the sequence in this clone withthe corresponding sequence of Ad11 DNA. The latter is obtained by directsequencing on Ad11 DNA using the indicated PCR primers. The large cosmidclone containing the Ad11 backbone is generated as follows. First, a PCRfragment is amplified on Ad11 DNA using the primers 35F5 and 35R6 withPwo DNA polymerase as described in Example 7 for Ad35 DNA. The PCRfragment is then purified using the PCR purification kit (LTI) anddigested with NotI and NdeI. The resulting 3.1 kb fragment is isolatedfrom gel using the GENECLEAN kit (Bio 101, Inc.). A second PCR fragmentis then generated on Ad11 DNA using the primers 35F7 and 35R8 (see,Example 7) with Pwo DNA polymerase according to the manufacturer'sinstructions and purified using the PCR purification kit (LTI). Thisamplified fragment is also digested with NdeI and NotI and the resulting1.6 kb fragment is purified from gel as previously described. The twodigested PCR fragments are then ligated together with cosmid vectorpWE15 previously digested with NotI and dephosphorylated using Tsapenzyme (LTI) according to manufacturer's instructions. One clone isselected that has one copy of both fragments inserted. Correct clonesare selected by analytical NotI digestion that gives a fragment of 4.7kb. Confirmation is obtained by a PCR reaction using primers 35F5 and35R8 that gives a fragment of the same size. The correct clone is thenlinearized with NdeI and isolated from gel. Next, wtAd11 DNA is digestedwith NdeI and the large 27 kb fragment is isolated from low meltingpoint agarose gel using agarase enzyme (Roche) according to themanufacturer's instructions. Both fragments are then ligated andpackaged using λ phage packaging extracts (Stratagene) according to themanufacturer's protocol. After infection into STBL-2 cells (LTI),colonies are grown on plates, and analyzed for the presence of thecomplete insert. The functionality of selected clones is then tested bycotransfection on PER.C6. Hereto, the DNA is digested with NotI and 6μgr is cotransfected with 2 μgr of a PCR fragment generated on Ad11 DNAwith primers 35F1 and 35R4 (see, Example 7). Correct clones give CPEwithin one week following transfection. The correct clone is designatedpWE.Ad11.pIX-rITR.

Using the previously described procedure, a plasmid-based systemconsisting of an adapter plasmid suitable for insertion of foreign genesand a large helper fragment containing the viral backbone is generated.Recombinant Ad11-based viruses are made using the methods describedherein for Ad35-based recombinant viruses.

Example 12 Neutralization of Adenoviruses in Samples Derived fromPatients

In the neutralization experiments described in Examples 1 and 5, allsamples were derived from healthy volunteers. Since one of theapplications of non-neutralized vectors is in the field of gene therapy,it is interesting to investigate whether Ad35 is also neutralized with alow frequency and with low titers in groups of patients that arecandidates for treatment with gene therapy.

Cardio-Vascular Disease Patients

26 paired serum and pericardial fluid (PF) samples were obtained frompatients with heart failure. These were tested against Ad5 and Ad35using the neutralization assay described in Example 1. The resultsconfirmed the previous data with samples from healthy volunteers. 70% ofthe serum samples contained NA to Ad5 and 4% to Ad35. In the pericardialfluid samples the titers were lower resulting in a total of 40% with NAto Ad5 and none to Ad35. There was a good correlation between NA in PFand serum, i.e., there were no positive PF samples without NA in thepaired serum sample. These results show that non-neutralized vectorsbased on Ad35 are preferred over Ad5 vectors for treatment ofcardio-vascular diseases. As is true for all forms of non-neutralizedvectors in this application, the vector may be based on the genome ofthe non-neutralized serotype or may be based on Ad5 (or anotherserotype) though displaying at least the major capsid proteins (hexon,penton and optionally fiber) of the non-neutralized serotype.

Rheumatoid Arthritis Patient

The molecular determinant underlying arthritis is presently not known,but both T-cell dysfunction and imbalanced growth factor production injoints is known to cause inflammation and hyperplasia of synovialtissue. The synoviocytes start to proliferate and invade the cartilageand bone that leads to destruction of these tissues. Current treatmentstarts (when in an early stage) with administration of anti-inflammatorydrugs (anti-TNF, IL1-RA, IL-10) and/or conventional drugs (e.g., MTX,sulfasalazine). In late stage RA, synovectomy is performed which isbased on surgery, radiation, or chemical intervention. An alternative oradditional option is treatment via gene therapy where an adenoviralvector is delivered directly into the joints of patients and expressesan anti-inflammatory drug or a suicide gene. Previous studies performedin rhesus monkeys suffering from collagen-induced arthritis have shownthat Ad5-based vectors carrying a marker gene can transducesynoviocytes. Whether in the human situation adenoviral delivery ishampered by the presence of NA is not known. To investigate the presenceof NA in the synovial fluid (“SF”) of RA patients, SF samples wereobtained from a panel of 53 randomly selected patients suffering fromRA. These were tested against several wt adenoviruses using theneutralization assay described in Example 1. Results of this screen arepresented in Table III. Adenovirus type 5 was found to be neutralized in72% of the SF samples. Most of these samples contain high titers of NAsince the highest dilution of the SF sample that was tested (64×)neutralized Ad5 viruses. This means that adenoviral vector delivery tothe synoviocytes in the joints of RA patients will be very inefficient.Moreover, since the titers in the SF are so high it is doubtful whetherlavage of the joints prior to vector injection will remove enough of theNA. Of the other serotypes that were tested, Ad35 was shown to beneutralized in only 4% of the samples. Therefore, these data confirm theresults obtained in serum samples from healthy patients and show that,for treatment of RA, Ad35-based vectors or chimeric vectors displayingat least some of the capsid proteins from Ad35 are preferred vectors.

Example 13 Modifications in the Backbone of Ad35-Based Viruses

Generation of pBr/Ad35.Pac-rITR and pBr/Ad35.PRn

Example 4 describes the generation of the Ad35 subclonepBr/Ad35.Eco13.3. This clone contains Ad35 sequences from bp 21943 tothe end of the right ITR cloned into the EcoRI and EcoRV sites ofpBr322. To extend these sequences to the PacI site located at bp 18137in Ad35, pBr/Ad35.Eco13.3 (see, Example 4) was digested with AatII andSnaBI and the large vector-containing fragment was isolated from gelusing the QIAEX II gel extraction kit (Qiagen). Ad35 wt DNA was digestedwith PacI and SnaBI and the 4.6 kb fragment was isolated as above. Thisfragment was then ligated to a double-stranded (“ds”) linker containinga PacI and an AatII overhang. This linker was obtained after annealingthe following oligonucleotides: A-P1: 5′-CTG GTG GTT AAT-3′ (SEQ IDNO:61) and A-P2: 5′-TAA CCA CCA GAC GT-3′ (SEQ ID NO:62).

The ligation mix containing the double stranded linker and thePacI-SnaBI Ad35 fragment was separated from unligated linker on a LMPgel. The 4.6 kb band was cut out of the gel, molten at 65° C., and thenligated to the purified pBr/Ad35.Eco13.3 vector fragment digested withAatII and SnaBI. Ligations were transformed into electrocompetent DH10Bcells (Life Technologies Inc.). The resulting clone, pBr/Ad35.Pac-rITR,contained Ad35 sequences from the PacI site at bp 18137 up to the rightITR.

Next, a unique restriction site was introduced at the 3′ end of theright ITR to be able to free the ITR from vector sequences. Hereto, aPCR fragment was used that covers Ad35 sequences from the NdeI site atbp 33165 to the right ITR having the restriction sites SwaI, NotI andEcoRI attached to the rITR. The PCR fragment was generated using primers35F7 and 35R8 (described in Example 7). After purification, the PCRfragment was cloned into the AT cloning vector (Invitrogen) andsequenced to verify correct amplification. The correct amplified clonewas then digested with EcoRI, blunted with Klenow enzyme andsubsequently digested with NdeI and the PCR fragment was isolated. Inparallel, the NdeI in the pBr vector in pBr/Ad35.Pac-rITR was removed asfollows: A pBr322 vector from which the NdeI site was removed bydigestion with NdeI, Klenow treatment and religation, was digested withAatII and NheI. The vector fragment was isolated in LMP gel and ligatedto the 16.7 kb Ad35 AatII-NheI fragment from pBr/Ad35.Pac-rITR that wasalso isolated in an LMP gel. This generated pBr/Ad35.Pac-rITR.ΔNdeI.Next, pBr/Ad35.Pac-rITR.ANdeI was digested with NheI, the ends werefilled in using Klenow enzyme, and the DNA was then digested with NdeI.The large fragment containing the vector and Ad35 sequences wasisolated. Ligation of this vector fragment and the PCR fragment resultedin pBr/Ad35.PRn. In this clone, specific sequences coding for fiber,E2A, E3, E4 or hexon can be manipulated. In addition, promoter sequencesthat drive, for instance, the E4 proteins or the E2 can be mutated ordeleted and exchanged for heterologous promoters.

2) Generation of Ad35-Based Viruses with Fiber Proteins from DifferentSerotypes

Adenoviruses infect human cells with different efficiencies. Infectionis accomplished by a two-step process involving both the fiber proteinsthat mediate binding of the virus to specific receptors on the cells,and the penton proteins that mediate internalization by interaction of,for example, the RGD sequence to integrins present on the cell surface.For subgroup B viruses, of which Ad35 is a member, the cellular receptorfor the fiber protein is not known. Striking differences exist ininfection efficiency of human cells of subgroup B viruses compared tosubgroup C viruses like Ad5 (see, International Patent Application WO00/03029 and European Patent Application EP 99200624.7). Even within onesubgroup, infection efficiencies of certain human cells may differbetween various serotypes. For example, the fiber of Ad16, when presenton an Ad5-based recombinant virus infects primary endothelial cells,smooth muscle cells and synoviocytes of human and rhesus monkey originbetter than Ad5 chimeric viruses carrying the fiber of Ad35 or Ad51.Thus, to obtain high infection efficiencies of Ad35-based viruses, itmay be necessary to change the fiber protein for a fiber protein of adifferent serotype. The technology for such fiber chimeras is describedfor Ad5-based viruses in Example 3, and is below exemplified for Ad35viruses.

First, most fiber sequences are deleted from the Ad35 backbone inconstruct pBr/Ad35.PRn as follows:

The left flanking sequences and part of the fiber protein in Ad35ranging from bp 30225 upstream of a unique MluI site up to bp 30872(numbers according to wt Ad35 sequence as disclosed in FIG. 6) in thetail of fiber are amplified using primers DF35-1: 5′-CAC TCA CCA CCT CCAATT CC-3′ (SEQ ID NO:63) and DF35-2: 5′-CGG GAT CCC GTA CGG GTA GAC AGGGTT GAA GG-3′ (SEQ ID NO:64).

This PCR amplification introduces a unique BsiWI site in the tail of thefiber gene. The right flanking sequences ranging from the end of thefiber protein at bp 31798 to bp 33199 (numbering according to wtAd35sequence, FIG. 6), 3′ from the unique NdeI site is amplified usingprimers DF35-3: 5′-CGG GAT CCG CTA GCT GAA ATA AAG TTT AAG TGT TTT TATTTA AAA TCA C-3′ (SEQ ID NO:65) and DF35-4: 5′-CCA GTT GCA TTG CTT GGTTGG-3′ (SEQ ID NO:66).

This PCR introduces a unique NheI site in the place of the fibersequences. PCR amplification is done with Pwo DNA polymerase (Roche)according to the manufacturer's instructions. After amplification, thePCR products are purified using a PCR purification kit and the fragmentsare digested with BamHI and ligated together. The 2 kb ligated fragmentsare purified from gel, and cloned in the PCR Script Amp vector(Stratagene). Correct amplification is checked by sequencing. The PCRfragment is then excised as an MluI/NdeI fragment and cloned inpBr/Ad35.PRn digested with the same enzymes. This generatespBr/Ad35.PRΔfib, a shuttle vector suitable to introduce fiber sequencesof alternative serotypes. This strategy is analogous to the fibermodification strategy for Ad5-based viruses as disclosed inInternational Patent Application WO00/03029. Primers that are listed inTable I of that application were used to amplify fiber sequences ofvarious subgroups of adenovirus. For amplification of fibers that arecloned in the pBr/Ad35.PRΔfib, the same (degenerate) primer sequencescan be used, however, the NdeI site in the forward primers (tailoligonucleotides A to E) should be changed to a BsiWI site and the NsiIsite in the reverse oligo (knob oligonucleotide 1 to 8) should bechanged in an NheI site. Thus, fiber 16 sequences are amplified usingthe following degenerate primers: 5′-CCK GTS TAC CCG TAC GAA GAT GAAAGC-3′ (SEQ ID NO:67) (where K can be a T or G and S can be a C or G asboth are degenerate oligo nucleotides) and 5′-CCG GCT AGC TCA GTC ATCTTC TCT GAT ATA-3′ (SEQ ID NO:68). Amplified sequences are then digestedwith BsiWI and NheI and cloned into pBr/Ad35.PRΔfib digested with thesame enzymes to generate pBr/Ad35.PRfib16. The latter construct is thendigested with PacI and SwaI and the insert is isolated from gel. ThePacI/SwaI Ad35 fragment with modified fiber is then cloned into thecorresponding sites of pWE/Ad35.pIX-rITR to givepWE/Ad35.pIX-rITR.fib16. This cosmid backbone can then be used with anAd35-based adapter plasmid to generate Ad35 recombinant viruses thatdisplay the fiber of Ad16. Other fiber sequences can be amplified with(degenerate) primers as mentioned above. If one of the fibers sequencesturns out to have an internal BsiWI or NheI site, the PCR fragment hasto be digested partially with that enzyme.

Generation of Ad35-Based Viruses with Inducible, E1 Independent, E4Expression

The adenovirus E4 promoter is activated by expression of E1 proteins. Itis unknown whether the Ad5 E1 proteins are capable of mediatingactivation of the Ad35 E4 promoter. Therefore, to enable production ofAd35 recombinant viruses on PER.C6 cells, it may be advantageous to makeE4 expression independent of E1. This can be achieved by replacing theAd35-E4 promoter by heterologous promoter sequences like, but notlimited to, the 7xTetO promoter.

Recombinant E1-deleted Ad5-based vectors are shown to have residualexpression of viral genes from the vector backbone in target cells,despite the absence of E1 expression. Viral gene expression increasesthe toxicity and may trigger a host immune response to the infectedcell. For most applications of adenoviral vectors in the field of genetherapy and vaccination, it is desired to reduce or diminish theexpression of viral genes from the backbone. One way to achieve this isto delete all, or as much as possible, sequences from the viralbackbone. By deleting E2A, E2B or E4 genes and/or the late genefunctions, one has to complement for these functions during production.This complementation can either be by means of a helper virus or throughstable addition of these functions, with or without inducibletranscription regulation, to the producer cell. Methods to achieve thishave been described for Ad5 and are known in the art. One specificmethod is replacement of the E4 promoter by promoter sequences that arenot active in the target cells. E4 proteins play a role in, for example,replication of adenoviruses through activation of the E2 promoter and inlate gene expression through regulation of splicing and nuclear exportof late gene transcripts. In addition, at least some of the E4 proteinsare toxic to cells. Therefore, reduction or elimination of E4 expressionin target cells will further improve Ad35-based vectors. One way toachieve this is to replace the E4 promoter by a heterologous promoterthat is inactive in the target cells. An example of a heterologouspromoter/activator system that is inactive in target cells is thetetracycline-inducible TetO system (Gossen and Bujard, 1992). Otherprokaryotic or synthetic promoter/activator systems may be used. In thisexample, the E4 promoter in the backbone of the viral vector is replacedby a DNA fragment containing 7 repeats of the tetracycline responsiveelement from the tet operon (7xTetO). A strong transactivator for thispromoter is a fusion protein containing the DNA binding domain of thetet repressor and the activation domain of VP16 (Tet transactivatorprotein, Tta). Strong E4 expression, independent of E1 expression, canbe accomplished in PER.C6 cells expressing Tta. Tta-expressing PER.C6cells have been generated and described (see, Example 15). Ad5 derivedE1-deleted viruses with E4 under control of 7xTetO can be generated andpropagated on these cells. Following infection in cells of human oranimal origin (that do not express the Tta transactivator), E4expression was found to be greatly diminished compared to E1 deletedviruses with the normal E4 promoter.

What follows is the construction of pWE/Ad35.pIX-rITR.TetO-E4, a cosmidhelper vector to produce viruses with the E4 promoter replacement.

First, a fragment was generated by PCR amplification on pBr/Ad35.PRn DNAusing the following primers: 355ITR: 5′-GAT CCG GAG CTC ACA ACG TCA TTTTCC CAC G-3′ (SEQ ID NO:69) and 353ITR: 5′-CGG AAT TCG CGG CCG CAT TTAAAT C-3′ (SEQ ID NO:70).

This fragment contains sequences between bp 34656 (numbering accordingto wtAd35) and the NotI site 3′ of the right ITR in pBr/Ad35.PRn andintroduces an SstI site 5′ of the right ITR sequence.

A second PCR fragment was generated on pBr/Ad35.PRn DNA using primers:

35DE4: (SEQ ID NO:71) 5′-CCC AAG CTT GCT TGT GTA TAT ATA TTG TGG-3′ and35F7: see, Example 7.

This PCR amplifies Ad35 sequences between bp 33098 and 34500 (numberingaccording to wtAd35) and introduces a HindIII site upstream of the E4Tata-box. With these two PCR reactions the right- and left-flankingsequences of the E4 promoter are amplified. For amplification, Pwo DNApolymerase was used according to manufacturer's instructions

A third fragment containing the 7xTetO promoter was isolated fromconstruct pAAO-E-TATA-7xTetO by digestion with SstI and HindIII. Thegeneration of pAAO-E-TATA-7xTetO is described below. The first PCRfragment (355/353) was then digested with SstI and NotI and ligated tothe 7xTetO fragment. The ligation mixture was then digested with HindIIIand NotI and the 0.5 kb fragment is isolated from gel. The second PCRfragment (35DE4/35F7) was digested with NdeI and HindIII and gelpurified. These two fragments were then ligated into pBr/Ad35.PRndigested with NdeI and NotI to give pBr/Ad35.PR.TetOE4. The modificationof the E4 promoter was then transferred to the Ad35 helper cosmid cloneby exchanging the PacI/SwaI fragment of the latter with the one frompBr/Ad35.PR.TetOE4 to give pWE/Ad35.pIX-rITR.TetOE4.

pAAO-E-TATA.7xTetO was generated as follows. Two oligonucleotides weresynthesized: TATAplus: 5′-AGC TTT CTT ATA AAT TTT CAG TGT TAG ACT AGTAAA TTG CTT AAG-3′ (SEQ. I.D. NO:72) and TATAmin: 5′-AGC TCT TAA GCA ATTTAC TAG TCT AAC ACT GAA AAT TTA TAA GAA-3′ (SEQ ID NO:73). (Theunderlined sequences form a modified TATA box).

The oligonucleotides were annealed to yield a double stranded DNAfragment with 5′ overhangs that are compatible with HindIII-digestedDNA. The product of the annealing reaction was ligated intoHindIII-digested pGL3-Enhancer Vector (Promega) to yield pAAO-E-TATA.The clone that had the HindIII site at the 5′ end of the insert restoredwas selected for further cloning.

Next, the heptamerized tet-operator sequence was amplified from theplasmid pUHC-13-3 (Gossen and Bujard, 1992) in a PCR reaction using theExpand PCR system (Roche) according to the manufacturer's protocol. Thefollowing primers were used: Tet3: 5′-CCG GAG CTC CAT GGC CTA ACT CGAGTT TAC CAC TCC C-3′ (SEQ ID NO:74) and Tet5: 5′-CCC AAG CTT AGC TCG ACTTTC ACT TTT CTC-3′ (SEQ ID NO:75).

The amplified fragment was digested with SstI and HindIII (these sitesare present in tet3 and tet5, respectively) and cloned intoSstI/HindIII-digested pAAO-E-TATA giving rise to pAAO-E-TATA-7xtetO.

To test the functionality of the generated pWE/Ad35.pIX-rITR.TetOE4cosmid clone, the DNA was digested with NotI. The left end of wtAd35 DNAwas then amplified using primers 35F1 and 35R4 (see, Example 7).Following amplification, the PCR mixture was purified and digested withSalI to remove intact viral DNA. Then 4 gr of both the digestedpWE/Ad35.pIX-rITR.TetOE4 and the PCR fragment was cotransfected intoPER.C6-tTA cells that were seeded in T25 flasks the day before.Transfected cells were transferred to T80 flasks after two days andanother two days later CPE was obtained, showing that the cosmidbackbone is functional.

Example 14 Generation of Cell Lines Capable of Complementing E1-DeletedAd35 Viruses Generation of pIG135 and pIG270

Construct pIG.E1A.E1B contains E1 region sequences of Ad5 correspondingto nucleotides 459 to 3510 of the wt Ad5 sequence (Genbank accessionnumber M72360) operatively linked to the human phosphoglycerate kinasepromoter (“PGK”) and the Hepatitis B Virus polyA sequences. Thegeneration of this construct is described in International PatentApplication No. WO97/00326. The E1 sequences of Ad5 were replaced bycorresponding sequences of Ad35 as follows. pRSV.Ad35-E1 (described inExample 8) was digested with EcoRI and Sse8387I and the 3 kb fragmentcorresponding to the Ad35 E1 sequences was isolated from gel. ConstructpIG.E1A.E1B was digested with Sse8387I completely and partially withEcoRI. The 4.2 kb fragment corresponding to vector sequences without theAd5 E1 region but retaining the PGK promoter were separated from otherfragments on LMP agarose gel and the correct band was excised from gel.Both obtained fragments were ligated resulting in pIG.Ad35-E1.

This vector was further modified to remove the LacZ sequences present inthe pUC119 vector backbone. Hereto, the vector was digested with BsaAIand BstXI and the large fragment was isolated from gel. A doublestranded oligo was prepared by annealing the following two oligos: BB1:5′-GTG CCT AGG CCA CGG GG-3′ (SEQ ID NO:76) and BB2: 5′-GTG GCC TAG GCAC-3′ (SEQ ID NO:77).

Ligation of the oligo and the vector fragment resulted in constructpIG135. Correct insertion of the oligo restores the BsaAI and BstXIsites and introduces a unique AvrII site. Next, we introduced a uniquesite at the 3′ end of the Ad35-E1 expression cassette in pIG135. Hereto,the construct was digested with SapI and the 3′ protruding ends weremade blunt by treatment with T4 DNA polymerase. The thus treated linearplasmid was further digested with BsrGI and the large vector-containingfragment was isolated from gel. To restore the 3′ end of the HBVpolyAsequence and to introduce a unique site, a PCR fragment was generatedusing the following primers: 270F:

(SEQ ID NO:78) 5′-CAC CTC TGC CTA ATC ATC TC-3′ and 270R: (SEQ ID NO:79)5′-GCT CTA GAA ATT CCA CTG CCT TCC ACC-3′.

The PCR was performed on pIG.Ad35.E1 DNA using Pwo polymerase (Roche)according to the manufacturer's instructions. The obtained PCR productwas digested with BsrGI and dephosphorylated using Tsap enzyme (LTI),the latter to prevent insert dimerization on the BsrGI site. The PCRfragment and the vector fragment were ligated to yield construct pIG270.

Ad35 E1 Sequences are Capable of Transforming Rat Primary Cells

Newborn WAG/RIJ rats were sacrificed at 1 week of gestation and kidneyswere isolated. After careful removal of the capsule, kidneys weredisintegrated into a single cell suspension by multiple rounds ofincubation in trypsin/EDTA (LTI) at 37° C. and collection of floatingcells in cold PBS containing 1% FBS. When most of the kidney wastrypsinized, all cells were re-suspended in DMEM supplemented with 10%FBS and filtered through a sterile cheesecloth. Baby Rat Kidney (BRK)cells obtained from one kidney were plated in five dishes (Greiner, 6cm). When a confluency of 70-80% was reached, the cells were transfectedwith 1 or 5 μgr DNA/dish using the CaPO₄ precipitation kit (LTI)according to the manufacturer's instructions. The following constructswere used in separate transfections: pIG.E1A.E1B (expressing the Ad5-E1region), pRSV.Ad35-E1, pIG.Ad35-E1 and pIG270 (the latter expressing theAd35-E1). Cells were incubated at 37° C., 5% CO₂ until foci oftransformed cells appeared. Table IV shows the number of foci thatresulted from several transfection experiments using circular or linearDNA. As expected, the Ad5-E1 region efficiently transformed BRK cells.Foci also appeared in the Ad35-E1 transfected cell layer although withlower efficiency. The Ad35 transformed foci appeared at a later timepoint: 2 weeks post transfection compared with seven to ten days forAd5-E1. These experiments clearly show that the E1 genes of the B groupvirus Ad35 are capable of transforming primary rodent cells. This provesthe functionality of the Ad35-E1 expression constructs and confirmsearlier findings of the transforming capacity of the B-group viruses Ad3and Ad7 (Dijkema, 1979). To test whether the cells in the foci werereally transformed a few foci were picked and expanded. From the sevenpicked foci, at least five turned out to grow as established cell lines.

Generation of New Packaging Cells Derived from Primary Human Amniocytes

Amniotic fluid obtained after amniocentesis was centrifuged and cellswere re-suspended in AmnioMax medium (LTI) and cultured in tissueculture flasks at 37° C. and 10% CO₂. When cells were growing nicely(approximately one cell division/24 hrs.), the medium was replaced witha 1:1 mixture of AmnioMax complete medium and DMEM low glucose medium(LTI) supplemented with Glutamax I (end concentration 4 mM, LTI) andglucose (end concentration 4.5 gr/L, LTI) and 10% FBS (LTI). Fortransfection ˜5×10⁵ cells were plated in 10 cm tissue culture dishes.The day after, cells were transfected with 20 μgr of circularpIG270/dish using the CaPO₄ transfection kit (LTI) according tomanufacturer's instructions and cells were incubated overnight with theDNA precipitate. The following day, cells were washed four times withPBS to remove the precipitate and further incubated for over three weeksuntil foci of transformed cells appeared. Once a week, the medium wasreplaced by fresh medium. Other transfection agents like, but notlimited to, LipofectAmine (LTI) or PEI (Polyethylenimine, high molecularweight, water-free, Aldrich) were used. Of these three agents PEIreached the best transfection efficiency on primary human amniocytes:˜1% blue cells 48 hours following transfection of pAdApt35.LacZ.

Foci are isolated as follows: The medium is removed and replaced by PBSafter which foci are isolated by gently scraping the cells using a50-200 μl Gilson pipette with a disposable filter tip. Cells containedin ˜10 μl PBS were brought in a 96 well plate containing 15 μltrypsin/EDTA (LTI) and a single cell suspension was obtained bypipetting up and down and a short incubation at room temperature. Afteraddition of 200 μl of the above described 1:1 mixture of AmnioMaxcomplete medium and DMEM with supplements and 10% FBS, cells werefurther incubated. Clones that continued to grow were expanded and theirability to complement growth of E1-deleted adenoviral vectors ofdifferent sub-groups was analyzed, specifically ones derived fromB-group viruses, specifically from Ad35 or Ad11.

Generation of New Packaging Cell Lines from HER Cells

HER cells were isolated and cultured in DMEM medium supplemented with10% FBS (LTI). The day before transfection, 5×10⁵ cells were plated in 6cm dishes and cultured overnight at 37° C. and 10% CO₂. Transfection wasdone using the CaPO₄ precipitation kit (LTI) according to themanufacturer's instructions. Each dish was transfected with 8-10 μgrpIG270 DNA, either as a circular plasmid or as a purified fragment. Toobtain the purified fragment, pIG270 was digested with AvrII and XbaIand the 4 kb fragment corresponding to the Ad35 E1 expression cassettewas isolated from gel by agarase treatment (Roche). The following day,the precipitate was washed away carefully by four washes with sterilePBS. Then fresh medium was added and transfected cells were furthercultured until foci of transformed cells appear. When large enough (>100cells) foci were picked and brought into 96-well plates as describedabove. Clones of transformed HER cells that continue to grow, wereexpanded and tested for their ability to complement growth of E1-deletedadenoviral vectors of different sub-groups specifically ones derivedfrom B-group viruses specifically from Ad35 or Ad11.

New Packaging Cell Lines Derived from PER.C6

As described in Example 8, it is possible to generate and grow Ad35E1-deleted viruses on PER.C6 cells with cotransfection of an Ad35-E1expression construct, e.g., pRSV.Ad35.E1. However, large-scaleproduction of recombinant adenoviruses using this method is cumbersomebecause, for each amplification step, a transfection of the Ad35-E1construct is needed. In addition, this method increases the risk ofnon-homologous recombination between the plasmid and the virus genomewith high chances of generation of recombinant viruses that incorporateE1 sequences resulting in replication competent viruses. To avoid this,the expression of Ad35-E1 proteins in PER.C6 has to be mediated byintegrated copies of the expression plasmid in the genome. Since PER.C6cells are already transformed and express Ad5-E1 proteins, addition ofextra Ad35-E1 expression may be toxic for the cells, however, it is notimpossible to stably transfect transformed cells with E1 proteins sinceAd5-E1 expressing A549 cells have been generated.

In an attempt to generate recombinant adenoviruses derived from subgroupB virus Ad7, Abrahamsen et al. (1997) were not able to generateE1-deleted viruses on 293 cells without contamination of wt Ad7. Virusesthat were picked after plaque purification on 293-ORF6 cells (Brough etal., 1996) were shown to have incorporated Ad7 E1B sequences bynon-homologous recombination. Thus, efficient propagation of Ad7recombinant viruses proved possible only in the presence of Ad7-E1Bexpression and Ad5-E4-ORF6 expression. The E1B proteins are known tointeract with cellular as well as viral proteins (Bridge et al., 1993;White, 1995). Possibly, the complex formed between the E1B 55K proteinand E4-ORF6 which is necessary to increase mRNA export of viral proteinsand to inhibit export of most cellular mRNAs, is critical and in someway serotype specific. The above experiments suggest that the E1Aproteins of Ad5 are capable of complementing an Ad7-E1A deletion andthat Ad7-E1B expression in adenovirus packaging cells on itself is notenough to generate a stable complementing cell line. To test whether oneor both of the Ad35-E1B proteins is/are the limiting factor in efficientAd35 vector propagation on PER.C6 cells, we have generated an Ad35adapter plasmid that does contain the E1B promoter and E1B sequences butlacks the promoter and the coding region for E1A. Hereto, the left endof wtAd35 DNA was amplified using the primers 35F1 and 35R4 (bothdescribed in Example 7) with Pwo DNA polymerase (Roche) according to themanufacturer's instructions. The 4.6 kb PCR product was purified usingthe PCR purification kit (LTI) and digested with SnaBI and ApaI enzymes.The resulting 4.2 kb fragment was then purified from gel using theQIAExII kit (Qiagen). Next, pAdApt35IP1 (Example 7) was digested withSnaBI and ApaI and the 2.6 kb vector-containing fragment was isolatedfrom gel using the GENECLEAN kit (BIO 101, Inc). Both isolated fragmentswere ligated to give pBr/Ad35.leftITR-pIX. Correct amplification duringPCR was verified by a functionality test as follows: The DNA wasdigested with BstBI to liberate the Ad35 insert from vector sequencesand 4 μgr of this DNA was cotransfected with 4 μgr of NotI-digestedpWE/Ad35.pIX-rITR (Example 7) into PER.C6 cells. The transfected cellswere passaged to T80 flasks at day 2 and again two days later CPE hadformed showing that the new pBr/Ad35.leftITR-pIX construct containsfunctional E1 sequences. The pBr/Ad35.leftITR-pIX construct was thenfurther modified as follows: The DNA was digested with SnaBI and HindIIIand the 5′ HindIII overhang was filled in using Klenow enzyme.Religation of the digested DNA and transformation into competent cells(LTI) gave construct pBr/Ad35leftITR-pIXΔE1A. This latter constructcontains the left end 4.6 kb of Ad35 except for E1A sequences between bp450 and 1341 (numbering according to wtAd35, FIG. 6) and thus lacks theE1A promoter and most of the E1A coding sequences.pBr/Ad35.leftITR-pIXΔE1A was then digested with BstBI and 2 μgr of thisconstruct was cotransfected with 6 μgr of NotI-digestedpWE/Ad35.pIX-rITR (Example 7) into PER.C6 cells. One week followingtransfection full CPE had formed in the transfected flasks.

This experiment shows that the Ad35-E1A proteins are functionallycomplemented by Ad5-e1A expression in PER.C6 cells and that at least oneof the Ad35-E1B proteins cannot be complemented by Ad5-E1 expression inPER.C6. It further shows that it is possible to make a complementingcell line for Ad35 E1-deleted viruses by expressing Ad35-E1B proteins inPER.C6. Stable expression of Ad35-E1B sequences from integrated copiesin the genome of PER.C6 cells may be driven by the E1B promoter andterminated by a heterologous poly-adenylation signal like, but notlimited to, the HBVpA. The heterologous pA signal is necessary to avoidoverlap between the E1B insert and the recombinant vector, since thenatural E1B termination is located in the pIX transcription unit thathas to be present on the adenoviral vector. Alternatively, the E1Bsequences may be driven by a heterologous promoter like, but not limitedto, the human PGK promoter or by an inducible promoter like, but notlimited to, the 7xtetO promoter (Gossen and Bujard, 1992). Also in thesecases the transcription termination is mediated by a heterologous pAsequence, e.g., the HBV pA. The Ad35-E1B sequences at least comprise oneof the coding regions of the E1B 21K and the E1B 55K proteins locatedbetween nucleotides 1611 and 3400 of the wtAd35 sequence. The insert mayalso include (part of the) Ad35-E1B sequences between nucleotides 1550and 1611 of the wt Ad35 sequence.

Example 15 Generation of Producer Cell Lines for the Production ofRecombinant Adenoviral Vectors Deleted in Early Region 1 and EarlyRegion 2A Generation of PER. C6-tTA Cells

Here is described the generation of cell lines for the production ofrecombinant adenoviral vectors that are deleted in early region 1 (E1)and early region 2A (E2A). The producer cell lines complement for the E1and E2A deletion from recombinant adenoviral vectors in trans byconstitutive expression of both E1 and E2A genes. The pre-establishedAd5-E1 transformed human embryo retinoblast (“HER”) cell line PER.C6(International Patent Appln. WO 97/00326) was further equipped with E2Aexpression cassettes.

The adenoviral E2A gene encodes a 72 kDa DNA Binding Protein with has ahigh affinity for single stranded DNA. Because of its function,constitutive expression of DBP is toxic for cells. The ts125E2A mutantencodes a DBP that has a Pro→Ser substitution of amino acid 413. Due tothis mutation, the ts125E2A encoded DBP is fully active at thepermissive temperature of 32° C., but does not bind to ssDNA at thenon-permissive temperature of 39° C. This allows the generation of celllines that constitutively express E2A, which is not functional and isnot toxic at the non-permissive temperature of 39° C. Temperaturesensitive E2A gradually becomes functional upon temperature decrease andbecomes fully functional at a temperature of 32° C., the permissivetemperature.

A. Generation of Plasmids Expressing the Wild Type E2A- orTemperature-Sensitive ts125E2A Gene.

pcDNA3 wtE2A: The complete wild-type early region 2A (E2A) coding regionwas amplified from the plasmid pBR/Ad.Bam-rITR (ECACC deposit P97082122)with the primers DBPpcr1 and DBPpcr2 using the Expand™ Long Template PCRsystem according to the standard protocol of the supplier (BoehringerMannheim). The PCR was performed on a Biometra Trio Thermoblock, usingthe following amplification program: 94° C. for two minutes, one cycle;94° C. for ten seconds +51° C. for 30 seconds +68° C. for two minutes,one cycle; 94° C. for ten seconds +58° C. for 30 seconds +68° C. for twominutes, ten cycles; 94° C. for ten seconds +58° C. for 30 seconds +68°C. for two minutes with ten seconds extension per cycle, 20 cycles; 68°C. for five minutes, one cycle. The primer DBPpcr1: CGG GAT CCG CCA CCATGG CCA GTC GGG AAG AGG AG (5′ to 3′) (SEQ ID NO: 80) contains a uniqueBamHI restriction site (underlined) 5′ of the Kozak sequence (italic)and start codon of the E2A coding sequence. The primer DBPpcr2: CGG AATTCT TAA AAA TCA AAG GGG TTC TGC CGC (5′ to 3′) (SEQ ID NO:81) contains aunique EcoRI restriction site (underlined) 3′ of the stop codon of theE2A coding sequence. The bold characters refer to sequences derived fromthe E2A coding region. The PCR fragment was digested with BamHI/EcoRIand cloned into BamHI/EcoRI-digested pcDNA3 (Invitrogen), giving rise topcDNA3 wtE2A.

pcDNA3tsE2A: The complete ts125E2A-coding region was amplified from DNAisolated from the temperature sensitive adenovirus mutant H5ts125. ThePCR amplification procedure was identical to that for the amplificationof wtE2A. The PCR fragment was digested with BamHI/EcoRI and cloned intoBamHI/EcoRI-digested pcDNA3 (Invitrogen), giving rise to pcDNA3tsE2A.The integrity of the coding sequence of wtE2A and tsE2A was confirmed bysequencing.

B. Growth Characteristics of Producer Cells for the Production ofRecombinant Adenoviral Vectors Cultured at 32°, 37° and 39° C.

PER.C6 cells were cultured in DMEM (Gibco BRL) supplemented with 10% FBS(Gibco BRL) and 10 mM MgCl₂ in a 10% CO₂ atmosphere at 32° C., 37° C. or39° C. At day 0, a total of 1×10⁶ PER.C6 cells were seeded per 25 cm²tissue culture flask (Nunc) and the cells were cultured at 32° C., 37°C. or 39° C. At days 1-8, cells were counted. FIG. 30 shows that thegrowth rate and the final cell density of the PER.C6 culture at 39° C.are comparable to that at 37° C. The growth rate and final density ofthe PER.C6 culture at 32° C. were slightly reduced as compared to thatat 37° C. or 39° C. No significant cell death was observed at any of theincubation temperatures. Thus, PER.C6 performs very well both at 32° C.and 39° C., the permissive and non-permissive temperature for ts125E2A,respectively.

C. Transfection of PER.C6 with E2A Expression Vectors; Colony Formationand Generation of Cell Lines

One day prior to transfection, 2×10⁶ PER.C6 cells were seeded per 6 cmtissue culture dish (Greiner) in DMEM, supplemented with 10% FBS and 10mM MgCl₂ and incubated at 37° C. in a 10% CO₂ atmosphere. The next day,the cells were transfected with 3, 5 or 8 μg of either pcDNA3, pcDNA3wtE2A or pcDNA3tsE2A plasmid DNA per dish, using the LipofectAMINE PLUSäReagent Kit according to the standard protocol of the supplier (GibcoBRL), except that the cells were transfected at 39° C. in a 10% CO₂atmosphere. After the transfection, the cells were constantly kept at39° C., the non-permissive temperature for ts125E2A. Three days later,the cells were put in DMEM supplemented with 10% FBS, 10 mM MgCl₂ and0.25 mg/ml G418 (Gibco BRL), and the first G418 resistant coloniesappeared at ten days post transfection. As shown in Table 1, there was adramatic difference between the total number of colonies obtained aftertransfection of pcDNA3 (˜200 colonies) or pcDNA3tsE2A (˜100 colonies)and pcDNA3wtE2A (only four colonies). These results indicate that thetoxicity of constitutively expressed E2A can be overcome by using atemperature sensitive mutant of E2A (ts125E2A) and culturing of thecells at the non-permissive temperature of 39° C.

From each transfection, a number of colonies were picked by scraping thecells from the dish with a pipette. The detached cells were subsequentlyput into 24-well tissue culture dishes (Greiner) and cultured further at39° C. in a 10% CO₂ atmosphere in DMEM, supplemented with 10% FBS, 10 mMMgCl₂ and 0.25 mg/ml G418. As shown in Table 1, 100% of the pcDNA3transfected colonies (4/4) and 82% of the pcDNA3tsE2A transfectedcolonies (37/45) were established to stable cell lines (the remainingeight pcDNA3tsE2A transfected colonies grew slowly and were discarded).In contrast, only one pcDNA3 wtE2A-transfected colony could beestablished. The other three died directly after picking.

Next, the E2A expression levels in the different cell lines weredetermined by Western blotting. The cell lines were seeded on 6-welltissue culture dishes and sub-confluent cultures were washed twice withPBS (NPBI) and lysed and scraped in RIPA (1% NP-40, 0.5% sodiumdeoxycholate and 0.1% SDS in PBS, supplemented with 1 mMphenylmethylsulfonylfluoride and 0.1 mg/ml trypsin inhibitor). After 15minutes incubation on ice, the lysates were cleared by centrifugation.Protein concentrations were determined by the Bio-Rad protein assay,according to standard procedures of the supplier (BioRad). Equal amountsof whole-cell extract were fractionated by SDS-PAGE on 10% gels.Proteins were transferred onto Immobilon-P membranes (Millipore) andincubated with the αDBP monoclonal antibody B6. The secondary antibodywas a horseradish-peroxidase-conjugated goat anti mouse antibody(BioRad). The Western blotting procedure and incubations were performedaccording to the protocol provided by Millipore. The complexes werevisualized with the ECL detection system according to the manufacturer'sprotocol (Amersham). FIG. 31 shows that all of the cell lines derivedfrom the pcDNA3tsE2A transfection expressed the 72-kDa E2A protein (leftpanel, lanes 4-14; middle panel, lanes 1-13; right panel, lanes 1-12).In contrast, the only cell line derived from the pcDNAwtE2A transfectiondid not express the E2A protein (left panel, lane 2). No E2A protein wasdetected in extract from a cell line derived from the pcDNA3transfection (left panel, lane 1), which served as a negative control.Extract from PER.C6 cells transiently transfected with pcDNA3ts125 (leftpanel, lane 3) served as a positive control for the Western blotprocedure. These data confirmed that constitutive expression of wtE2A istoxic for cells and that using the ts125 mutant of E2A could circumventthis toxicity.

D. Complementation of E2A Deletion in Adenoviral Vectors on PER.C6 CellsConstitutively Expressing Full-Length ts125E2A

The adenovirus Ad5.dl802 is an Ad5 derived vector deleted for the majorpart of the E2A coding region and does not produce functional DBP.Ad5.dl802 was used to test the E2A trans-complementing activity ofPER.C6 cells constitutively expressing ts125E2A. Parental PER.C6 cellsor PER.C6tsE2A clone 3-9 were cultured in DMEM, supplemented with 10%FBS and 10 mM MgCl₂ at 39° C. and 10% CO₂ in 25 cm² flasks and eithermock-infected or infected with Ad5.dl802 at an m.o.i. of 5. Subsequentlythe infected cells were cultured at 32° C. and cells were screened forthe appearance of a cytopathic effect (“CPE”) as determined by changesin cell morphology and detachment of the cells from the flask. Full CPEappeared in the Ad5.dl802 infected PER.C6tsE2A clone 3-9 within twodays. No CPE appeared in the Ad5.dl802 infected PER.C6 cells or themock-infected cells. These data showed that PER.C6 cells constitutivelyexpressing ts125E2A complemented in trans for the E2A deletion in theAd5.dl802 vector at the permissive temperature of 32° C.

E. Serum-Free Suspension Culture of PER.C6tsE2A Cell Lines

Large-scale production of recombinant adenoviral vectors for human genetherapy requires an easy and scaleable culturing method for the producercell line, preferably a suspension culture in medium devoid of any humanor animal constituents. To that end, the cell line PER.C6tsE2A c5-9(designated c5-9) was cultured at 39° C. and 10% CO₂ in a 175 cm² tissueculture flask (Nunc) in DMEM, supplemented with 10% FBS and 10 mM MgCl₂.At sub-confluency (70-80% confluent), the cells were washed with PBS(NPBI) and the medium was replaced by 25 ml serum free suspension mediumEx-cell™ 525 (JRH) supplemented with 1×L-Glutamine (Gibco BRL),hereafter designated SFM. Two days later, cells were detached from theflask by flicking and the cells were centrifuged at 1,000 rpm for fiveminutes. The cell pellet was re-suspended in 5 ml SFM and 0.5 ml cellsuspension was transferred to a 80 cm² tissue culture flask (Nunc),together with 12 ml fresh SFM. After two days, cells were harvested (allcells are in suspension) and counted in a Burker cell counter. Next,cells were seeded in a 125 ml tissue culture Erlenmeyer (Corning) at aseeding density of 3×10⁵ cells per ml in a total volume of 20 ml SFM.Cells were further cultured at 125 RPM on an orbital shaker (GFL) at 39°C. in a 10% CO₂ atmosphere. Cells were counted at day 1-6 in a Burkercell counter. In FIG. 4, the mean growth curve from eight cultures isshown. PER.C6tsE2A c5-9 performed well in serum free suspension culture.The maximum cell density of approximately 2×10⁶ cells per ml is reachedwithin five days of culture.

F. Growth Characteristics of PER.C6 and PER.C6/E2A at 37° C. and 39° C.

PER.C6 cells or PER.C6ts125E2A (c8-4) cells were cultured in DMEM (GibcoBRL) supplemented with 10% FBS (Gibco BRL) and 10 mM MgCl₂ in a 10% CO₂atmosphere at either 37° C. (PER.C6) or 39° C. (PER.C6ts125E2A c8-4). Atday 0, a total of 1×10⁶ cells were seeded per 25 cm² tissue cultureflask (Nunc) and the cells were cultured at the respective temperatures.At the indicated time points, cells were counted. The growth of PER.C6cells at 37° C. was comparable to the growth of PER.C6ts125E2A c8-4 at39° C. (FIG. 33). This shows that constitutive expression of ts125E2Aencoded DBP had no adverse effect on the growth of cells at thenon-permissive temperature of 39° C.

G. Stability of PER.C6ts125E2A

For several passages, the PER.C6ts125E2A cell line clone 8-4 wascultured at 39° C. and 10% CO₂ in a 25 cm² tissue culture flask (Nunc)in DMEM, supplemented with 10% FBS and 10 mM MgCl₂ in the absence ofselection pressure (G418). At sub-confluency (70-80% confluent), thecells were washed with PBS (NPBI) and lysed and scraped in RIPA (1%NP-40, 0.5% sodium deoxycholate and 0.1% SDS in PBS, supplemented with 1mM phenylmethylsulfonylfluoride and 0.1 mg/ml trypsin inhibitor). After15 minutes incubation on ice, the lysates were cleared bycentrifugation. Protein concentrations were determined by the BioRadprotein assay, according to standard procedures of the supplier(BioRad). Equal amounts of whole-cell extract were fractionated bySDS-PAGE in 10% gels. Proteins were transferred onto Immobilon-Pmembranes (Millipore) and incubated with the αDBP monoclonal antibodyB6. The secondary antibody was a horseradish-peroxidase-conjugated goatanti mouse antibody (BioRad). The Western blotting procedure andincubations were performed according to the protocol provided byMillipore. The complexes were visualized with the ECL detection systemaccording to the manufacturer's protocol (Amersham). The expression ofts125E2A encoded DBP was stable for at least 16 passages, which isequivalent to approximately 40 cell doublings (FIG. 34). No decrease inDBP levels was observed during this culture period, indicating that theexpression of ts125E2A was stable, even in the absence of G418 selectionpressure.

Example 16 Generation of tTA Expressing Packaging Cell Lines

A. Generation of a Plasmid from which the tTa Gene is ExpressedpcDNA3.1-tTA: The tTA gene, a fusion of the tetR and VP16 genes, wasremoved from the plasmid pUHD 15-1 (Gossen and Bujard, 1992) bydigestion using the restriction enzymes BamHI and EcoRI. First, pUHD15-1was digested with EcoRI. The linearized plasmid was treated with Klenowenzyme in the presence of dNTPs to fill in the EcoRI sticky ends. Then,the plasmid was digested with BamHI. The resulting fragment, 1025 bp inlength, was purified from agarose. Subsequently, the fragment was usedin a ligation reaction with BamHI/EcoRV-digested pcDNA 3.1 HYGRO (−)(Invitrogen) giving rise to pcDNA3.1-tTA. After transformation intocompetent E. Coli DH5α (Life Techn.) and analysis of ampicillinresistant colonies, one clone was selected that showed a digestionpattern as expected for pcDNA3.1-tTA.

B. Transfection of PER.C6 and PER.C6/E2A with the tTA Expression Vector;Colony Formation and Generation of Cell Lines

One day prior to transfection, 2×10⁶ PER.C6 or PER.C6/E2A cells wereseeded per 60 mm tissue culture dish (Greiner) in Dulbecco's modifiedessential medium (DMEM, Gibco BRL) supplemented with 10% FBS (JRH) and10 mM MgCl₂ and incubated at 37° C. in a 10% CO₂ atmosphere. The nextday, cells were transfected with 4-8 μg of pcDNA3.1-tTA plasmid DNAusing the LipofectAMINE PLUS™ Reagent Kit according to the standardprotocol of the supplier (Gibco BRL). The cells were incubated with theLipofectAMINE PLUS™-DNA mixture for four hours at 37° C. and 10% CO₂.Then, 2 ml of DMEM supplemented with 20% FBS and 10 mM MgCl₂ was addedand cells were further incubated at 37° C. and 10% CO₂. The next day,cells were washed with PBS and incubated in fresh DMEM supplemented with10% FBS, 10 mM MgCl₂ at either 37° C. (PER.C6) or 39° C. (Per.C6/E2A) ina 10% CO₂ atmosphere for three days. Then, the media were exchanged forselection media; PER.C6 cells were incubated with DMEM supplemented with10% FBS, 10 mM MgCl₂ and 50 μg/ml hygromycin B (GIBCO) while PER.C6/E2Acells were maintained in DMEM supplemented with 10% FBS, 10 mM MgCl₂ and100 μg/ml hygromycin B. Colonies of cells that resisted the selectionappeared within three weeks while nonresistant cells died during thisperiod.

From each transfection, a number of independent, hygromycin-resistantcell colonies were picked by scraping the cells from the dish with apipette and put into 2.5 cm² dishes (Greiner) for further growth in DMEMcontaining 10% FBS, 10 mM MgCl₂ and supplemented with 50 μg/ml (PERC.6cells) or 100 μg/ml (PERC.6/E2A cells) hygromycin in a 10% CO₂atmosphere and at 37° C. or 39° C., respectively.

Next, it was determined whether these hygromycin-resistant cell coloniesexpressed functional tTA protein. Therefore, cultures of PER.C6/tTA orPER/E2A/tTA cells were transfected with the plasmid pUHC 13-3 thatcontains the reporter gene luciferase under the control of the 7xtetOpromoter (Gossens and Bujard, 1992). To demonstrate that the expressionof luciferase was mediated by tTA, one half of the cultures weremaintained in medium without doxycycline. The other half was maintainedin medium with 8 g/ml doxycycline (Sigma). The latter drug is ananalogue of tetracycline and binds to tTA and inhibits its activity. AllPER.C6/tTA and PER/E2A/tTA cell lines yielded high levels of luciferase,indicating that all cell lines expressed the tTA protein (FIG. 35). Inaddition, the expression of luciferase was greatly suppressed when thecells were treated with doxycycline. Collectively, the data showed thatthe isolated and established hygromycin-resistant PER.C6 and PER/E2Acell clones all expressed functional tTA.

TABLE I Elution log₁₀ Serotype [NaCl] mM VP/ml CCID50 VP/CCID50 ratio 1597 8.66 × 10¹⁰ 5.00 × 10⁷ 3.2 2 574 1.04 × 10¹² 3.66 × 10¹¹ 0.4 3 1311.19 × 10¹¹ 1.28 × 10⁷ 4.0 4 260 4.84 × 10¹¹ 2.50 × 10⁸ 3.3 5 533 5.40 ×10¹¹ 1.12 × 10¹⁰ 1.7 6 477 1.05 × 10¹² 2.14 × 10¹⁰ 1.7 7 328 1.68 × 10¹²2.73 × 10⁹ 2.4 9 379 4.99 × 10¹¹ 3.75 × 10⁷ 4.1 10 387 8.32 × 10¹² 1.12× 10⁹ 3.9 12 305 3.64 × 10¹¹ 1.46 × 10⁷ 4.4 13 231 4.37 × 10¹² 7.31 ×10⁸ 3.8 15 443 5.33 × 10¹² 1.25 × 10⁹ 3.6 16 312 1.75 × 10¹² 5.59 × 10⁸3.5 17 478 1.39 × 10¹² 1.45 × 10⁹ 3.0 19 430 8.44 × 10¹¹ 8.55 × 10⁷ 4.020 156 1.41 × 10¹¹ 1.68 × 10⁷ 3.9 21 437 3.21 × 10¹¹ 1.12 × 10⁸ 3.5 22365 1.43 × 10¹² 5.59 × 10⁷ 3.4 23 132 2.33 × 10¹¹ 1.57 × 10⁷ 4.2 24 4055.12 × 10¹² 4.27 × 10⁸ 4.1 25 405 7.24 × 10¹¹ 5.59 × 10⁷ 4.1 26 356 1.13× 10¹² 1.12 × 10⁸ 4.0 27 342 2.00 × 10¹² 1.28 × 10⁸ 4.2 28 347 2.77 ×10¹² 5.00 × 10⁷ 4.7 29 386 2.78 × 10¹¹ 2.00 × 10⁷ 4.1 30 409 1.33 × 10¹²5.59 × 10⁸ 3.4 31 303 8.48 × 10¹⁰ 2.19 × 10⁷ 3.6 33 302 1.02 × 10¹² 1.12× 10⁷ 5.0 34 425 1.08 × 10¹² 1.63 × 10¹¹ 0.8 35 446 3.26 × 10¹² 1.25 ×10¹¹ 1.4 36 325 9.26 × 10¹² 3.62 × 10⁹ 3.4 37 257 5.86 × 10¹²  2.8 × 10⁹3.3 38 337 3.61 × 10¹² 5.59 × 10⁷ 4.8 39 241 3.34 × 10¹¹ 1.17 × 10⁷ 4.542 370 1.95 × 10¹² 1.12 × 10⁸ 4.2 43 284 2.42 × 10¹² 1.81 × 10⁸ 4.1 44295 8.45 × 10¹¹ 2.00 × 10⁷ 4.6 45 283 5.20 × 10¹¹ 2.99 × 10⁷ 4.2 46 2829.73 × 10¹² 2.50 × 10⁸ 4.6 47 271 5.69 × 10¹¹ 3.42 × 10⁷ 4.2 48 264 1.68× 10¹² 9.56 × 10⁸ 3.3 49 332 2.20 × 10¹² 8.55 × 10⁷ 4.4 50 459 7.38 ×10¹² 2.80 × 10⁹ 3.4 51 450 8.41 × 10¹¹ 1.88 × 10⁸ 3.7

Legend to Table I:

All human adenoviruses used in the neutralization experiments wereproduced on PER.C6 cells (Fallaux et al., 1998) and purified on CsCl asdescribed in example 1. The NaCl concentration at which the differentserotypes eluted from the HPLC column is shown. Virus particles/ml(VP/ml) were calculated from an Ad5 standard. The titer in theexperiment (CCID50) was determined on PER.C6 cells as described inExample 1 by titrations performed in parallel with the neutralizationexperiment. The CCID50 is shown for the 44 viruses used in this studyand reflects the dilution of the virus needed to obtain CPE in 50% ofthe wells after five days. The ratio of VP/CCID50 is depicted in log₁₀and is a measurement of the infectivity of the different batches onPER.C6 cells.

TABLE II AdApt35.LacZ viruses escape neutralization by human serum.Human serum dilution no Virus serum 10x 50x 250x 1250x 6250x AdApt5.LacZ100% 0% 0% 1% 40% 80% moi: 5 VP/cell AdApt35.LacZ 100% 100%  100%  100% 100%  100%  250 μl crude lysate

TABLE III Percentage of synovial fluid samples containing neutralizingactivity (NA) to wt adenoviruses of different serotypes. % of SF sampleswith NA % of SF samples with NA (all positives) (positives at ≧64xdilution) Ad5 72 59 Ad26 66 34 Ad34 45 19 Ad35 4 0 Ad48 42 4

TABLE IV The numbers of foci obtained with the different E1 expressionconstructs in BRK transformation experiments. Average # of foci/dish:Construct 1 μgr 5 μgr Experiment 1 pIG.E1A.E1B nd 60 pIG.E1A.E1B nd 35pRSVAd35E1 0 3 pIG.Ad35.E1 3 7 Experiment 2 pIG.E1A.E1B 37 ndpIG.Ad35.E1 nd 2 Experiment 3 pIG.E1A.E1B nd 140 pIG.Ad35.E1 nd 20pIG270 nd 30

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1.-62. (canceled)
 64. A method of avoiding pre-existing adenoviralneutralizing activity in a human subject, the method comprising:obtaining a recombinant, replication-defective adenovirus comprising anadenoviral genome comprising a nucleic acid of interest operably linkedto a promoter; and administering the adenovirus to the human subject,wherein infection of cells by the adenovirus in the presence of serumobtained from a population of human volunteers is neutralized orinhibited by less than 40% compared to infection by the adenovirus inthe absence of the serum, wherein neutralization or inhibition ofinfection is due to antibodies present in the serum.
 65. The methodaccording to claim 64, wherein the recombinant, replication-defectiveadenovirus is selected from the group of adenovirus serotypes consistingof Ad11, Ad26, Ad34, Ad35, Ad48, and Ad49.
 66. The method according toclaim 64, wherein the adenoviral genome comprises a deletion in the E1region rendering the adenovirus replication-defective, and wherein thenucleic acid of interest is present in the deleted E1 region.
 67. Amethod of avoiding pre-existing adenoviral neutralizing activity in ahuman subject, the method comprising: determining neutralization orinhibition of an adenovirus in an in vitro cellular infectionneutralization assay, wherein infection of cells is performed in thepresence and in the absence of serum obtained from a population of humanvolunteers; selecting an adenovirus serotype that is neutralized orinhibited in infection by less than 40% compared to infection in theabsence of the serum; producing a recombinant, replication-defectiveadenovirus of the selected adenovirus serotype, the recombinant,replication-defective adenovirus comprising an adenoviral genomecomprising a nucleic acid of interest operably linked to a promoter; andadministering the recombinant, replication-defective adenovirus to thehuman subject.
 68. The method according to claim 67, wherein therecombinant, replication-defective adenovirus is selected from the groupof adenovirus serotypes consisting of Ad11, Ad26, Ad34, Ad35, Ad48, andAd49.
 69. The method according to claim 67, wherein the adenoviralgenome comprises a deletion in the E1 region rendering the adenovirusreplication-defective, and wherein the nucleic acid of interest ispresent in the deleted E1 region.